diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 5663 |
1 files changed, 3834 insertions, 1829 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f567e22a48..de500f5441 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -50,6 +50,7 @@ #:use-module (gnu packages curl) #:use-module (gnu packages docker) #:use-module (gnu packages gcc) + #:use-module (gnu packages ghostscript) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) @@ -64,6 +65,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) #:use-module (gnu packages statistics) + #:use-module (gnu packages tex) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xml) @@ -72,6 +74,29 @@ ;;; Annotations +(define-public r-bsgenome-drerio-ucsc-danrer7 + (package + (name "r-bsgenome-drerio-ucsc-danrer7") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer7" version + 'annotation)) + (sha256 + (base32 "17x3hj08jag05y8q4aziy455jy15dpwkdbh97v3byzcda0kpwbpg")))) + (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer7"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome)) + (home-page + "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer7") + (synopsis "Full genome sequences for Danio rerio (UCSC version danRer7)") + (description + "This package provides full genome sequences for Danio rerio (Zebrafish) +as provided by UCSC (@code{danRer7}, Jul. 2010) and stored in Biostrings +objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-ucsc-hg38-masked (package (name "r-bsgenome-hsapiens-ucsc-hg38-masked") @@ -128,6 +153,134 @@ in @code{MaskedDNAString} objects.") Ensembl.") (license license:artistic2.0))) +(define-public r-genomewidesnp6crlmm + (package + (name "r-genomewidesnp6crlmm") + (version "1.0.7") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "genomewidesnp6Crlmm" version + 'annotation)) + (sha256 + (base32 "16qcxa32fmbdcv5dck0grsnqyfcqql7wpxa1l6andv9hrvabv2jx")))) + (properties `((upstream-name . "genomewidesnp6Crlmm"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/genomewidesnp6Crlmm") + (synopsis "Metadata for fast genotyping with the crlmm package") + (description + "This is a package with metadata for fast genotyping Affymetrix +@code{GenomeWideSnp_6} arrays using the @code{crlmm} package.") + (license license:artistic2.0))) + +(define-public r-hgu95a-db + (package + (name "r-hgu95a-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hgu95a.db" version + 'annotation)) + (sha256 + (base32 "1krmnl5kqfvb4jvrqy72x0s8z7rha96d5nwcbnarpflf12k4hrha")))) + (properties `((upstream-name . "hgu95a.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (native-inputs (list r-runit)) + (home-page "https://bioconductor.org/packages/hgu95a.db") + (synopsis "Affymetrix HG_U95A Array annotation data (chip hgu95a)") + (description + "This package provides Affymetrix HG_U95A Array annotation data (chip +hgu95a) assembled using data from public repositories.") + (license license:artistic2.0))) + +(define-public r-hgu95av2 + (package + (name "r-hgu95av2") + (version "2.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hgu95av2" version + 'annotation)) + (sha256 + (base32 "181bady90v89yx2gzwahhcl63aiypcx33pkfnjxkyq45qgb18bqi")))) + (properties `((upstream-name . "hgu95av2"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/hgu95av2") + (synopsis "Affymetrix Human Genome U95 Set annotation data (hgu95av2)") + (description + "This package provides Affymetrix Human Genome U95 Set annotation +data (hgu95av2) assembled using data from public data repositories.") + (license license:artistic2.0))) + +(define-public r-hgu95av2-db + (package + (name "r-hgu95av2-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hgu95av2.db" version + 'annotation)) + (sha256 + (base32 "1zk3mb9p8z2xabqr6y9jdiwidjzkgn22jlqyqg1bq0iahmj2ywpz")))) + (properties `((upstream-name . "hgu95av2.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (native-inputs (list r-runit)) + (home-page "https://bioconductor.org/packages/hgu95av2.db") + (synopsis + "Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)") + (description + "This package provides Affymetrix HG_U95Av2 Array annotation +data (chip hgu95av2) assembled using data from public repositories.") + (license license:artistic2.0))) + +(define-public r-hgu95av2cdf + (package + (name "r-hgu95av2cdf") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hgu95av2cdf" version + 'annotation)) + (sha256 + (base32 "1zp1y5awnkprkmk01rmn881y50bslfi8s33i8bws39am5xma0jfl")))) + (properties `((upstream-name . "hgu95av2cdf"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi)) + (home-page "https://bioconductor.org/packages/hgu95av2cdf") + (synopsis "hgu95av2cdf") + (description + "This package provides a package containing an environment representing +the HG_U95Av2.CDF file.") + (license license:lgpl2.0+))) + +(define-public r-hgu133a-db + (package + (name "r-hgu133a-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hgu133a.db" version + 'annotation)) + (sha256 + (base32 "00jcginfs161ls9hxsvynbrghg3awjrphnc54b8g0gj8g6x22pll")))) + (properties `((upstream-name . "hgu133a.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (native-inputs (list r-runit)) + (home-page "https://bioconductor.org/packages/hgu133a.db") + (synopsis "Affymetrix HG-U133A Array annotation data (chip hgu133a)") + (description + "This package provides Affymetrix HG-U133A Array annotation data (chip +hgu133a) assembled using data from public repositories.") + (license license:artistic2.0))) + (define-public r-hpo-db (package (name "r-hpo-db") @@ -163,6 +316,7 @@ Ensembl.") (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi)) (native-inputs `(("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) ("HPO.sqlite" ,(origin (method url-fetch) @@ -181,6 +335,47 @@ descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.") (license license:artistic2.0))) +(define-public r-human370v1ccrlmm + (package + (name "r-human370v1ccrlmm") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "human370v1cCrlmm" version + 'annotation)) + (sha256 + (base32 "1fhvgc6phhy8fqrl8bwjyskjl95bwlc08jyrkhsivml3ngbsfdf7")))) + (properties `((upstream-name . "human370v1cCrlmm"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/human370v1cCrlmm") + (synopsis "Metadata for fast genotyping with the 'crlmm' package") + (description + "This is a package with metadata for genotyping Illumina 370k arrays +using the crlmm package.") + (license license:artistic2.0))) + +(define-public r-illuminahumanmethylationepicanno-ilm10b2-hg19 + (package + (name "r-illuminahumanmethylationepicanno-ilm10b2-hg19") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" + version + 'annotation)) + (sha256 + (base32 "0sfdx0lpiw3l4passx93pjfswd0iv3hxdc7ciazh53baib3xpv2d")))) + (properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b2.hg19"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (home-page "https://bitbucket.com/kasperdanielhansen/Illumina_EPIC") + (synopsis "Annotation for Illumina's EPIC methylation arrays") + (description + "This is an annotation package for Illumina's EPIC methylation arrays.") + (license license:artistic2.0))) + (define-public r-jaspar2020 (package (name "r-jaspar2020") @@ -200,6 +395,34 @@ functions for previous uncharacteried genes and alleles.") utilize the TFBSTools package (version 1.23.1 or higher).") (license license:gpl2))) +(define-public r-mafdb-1kgenomes-phase1-hs37d5 + (package + (name "r-mafdb-1kgenomes-phase1-hs37d5") + (version "3.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MafDb.1Kgenomes.phase1.hs37d5" version + 'annotation)) + (sha256 + (base32 "0vsjik59qa36w402bcrd5z27wc9vyp4gl0ffcwskd9iwjqim0phi")))) + (properties `((upstream-name . "MafDb.1Kgenomes.phase1.hs37d5"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors)) + (home-page + "https://bioconductor.org/packages/MafDb.1Kgenomes.phase1.hs37d5") + (synopsis + "Minor allele frequency data from 1000 Genomes Phase 1 for hs37d5") + (description + "Store minor allele frequency data from the Phase 1 of the 1000 Genomes +Project for the human genome version hs37d5.") + (license license:artistic2.0))) + (define-public r-mafh5-gnomad-v3-1-2-grch38 (package (name "r-mafh5-gnomad-v3-1-2-grch38") @@ -233,14 +456,14 @@ It retrieves this data from the Genome Aggregation Database (define-public r-mpo-db (package (name "r-mpo-db") - (version "0.99.7") + (version "0.99.8") (source (origin (method url-fetch) (uri (bioconductor-uri "MPO.db" version 'annotation)) (sha256 - (base32 "0x1rcikg189akbd71yh0p02482km9hry6i69s2srdf5mlgqficvl")))) + (base32 "1aaz4s8ydcqxx5qwfqxxs7fc20bjbdjxzg700gwd59kjgk6ijm92")))) (properties `((upstream-name . "MPO.db"))) (build-system r-build-system) (arguments @@ -257,7 +480,7 @@ It retrieves this data from the Genome Aggregation Database (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m) (string-append "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };")) - (("dbfile <- ah.*" m) + (("dbfile <- ah\\[\\[\"AH117057\".*" m) (string-append "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \"" file "\";} else { " m " }\n"))))))))) @@ -265,6 +488,7 @@ It retrieves this data from the Genome Aggregation Database (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi)) (native-inputs `(("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) ("MPO.sqlite" ,(origin (method url-fetch) @@ -273,7 +497,7 @@ It retrieves this data from the Genome Aggregation Database (sha256 (base32 "12rf5dpnjrpw55bgnbn68dni2g0p87nvs9c7mamqk0ayafs61zl0")))))) (home-page "https://github.com/YuLab-SMU/MPO.db") - (synopsis "set of annotation maps describing the Mouse Phenotype Ontology") + (synopsis "Set of annotation maps describing the Mouse Phenotype Ontology") (description "This is the human disease ontology R package HDO.db, which provides the semantic relationship between human diseases. Relying on the DOSE and @@ -289,21 +513,44 @@ Using the same principle to diseases can identify genetic associations and even help to identify disease associations that are not obvious.") (license license:artistic2.0))) +(define-public r-oligodata + (package + (name "r-oligodata") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "oligoData" version + 'annotation)) + (sha256 + (base32 "1d1yfms3jv2c4s255xnh8yxwijrj35skw3nxds7l46y88lg3qn8y")))) + (properties `((upstream-name . "oligoData"))) + (build-system r-build-system) + (propagated-inputs (list r-oligo)) + (home-page "https://bioconductor.org/packages/oligoData") + (synopsis "Dataset samples for the oligo package") + (description + "This package provides dataset samples (Affymetrix: Expression, Gene, +Exon, SNP; @code{NimbleGen}: Expression, Tiling) to be used with the +@code{oligo} package.") + (license license:lgpl2.0+))) + (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) (sha256 - (base32 "1af2yrbpn58z34jq39qmmwprzsffgxbrs84dsxny4rksa8k6j70s")))) + (base32 "0qd6ppvcpsprbw8c9rp3fx5i8cs6gv0n4mqwxwjs1421p19m1bqd")))) (properties `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") (synopsis "Genome wide annotation for E coli strain K12") (description @@ -319,7 +566,7 @@ analysis.") (define-public r-org-bt-eg-db (package (name "r-org-bt-eg-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) @@ -329,11 +576,12 @@ analysis.") 'annotation)) (sha256 (base32 - "0rbbjv47fadc6jgpqrimsd91f35fw6sw8d805vf61nx5xhbl3lpc")))) + "0ryfpblhpqzkww1xb63k2c5ki8xh73as8fwl8f8kvsy4x7axfr5g")))) (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/org.Bt.eg.db") (synopsis "Genome wide annotation for Bovine") (description @@ -344,17 +592,18 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-sc-sgd-db (package (name "r-org-sc-sgd-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Sc.sgd.db" version 'annotation)) (sha256 - (base32 "1sbjwyf0ibivdhhxsaljgqa4lqp3hcf8gcrlcm2vd78bfm5cm7bg")))) + (base32 "0p7mvra93l21pb14qbvqjg7pwl6n572d8a3k15v9fsafikd07v8a")))) (properties `((upstream-name . "org.Sc.sgd.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/org.Sc.sgd.db") (synopsis "Genome wide annotation for Yeast") (description @@ -363,6 +612,32 @@ on mapping using ORF identifiers from @acronym{SGD, Saccharomyces Genome Database}.") (license license:artistic2.0))) +(define-public r-pd-mapping50k-hind240 + (package + (name "r-pd-mapping50k-hind240") + (version "3.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pd.mapping50k.hind240" version + 'annotation)) + (sha256 + (base32 "1whpjdr4aql846cm8nzgs613pi12qdqfixhqcfv8wrqyks27kq6s")))) + (properties `((upstream-name . "pd.mapping50k.hind240"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings + r-dbi + r-iranges + r-oligo + r-oligoclasses + r-rsqlite + r-s4vectors)) + (home-page "https://bioconductor.org/packages/pd.mapping50k.hind240") + (synopsis "Platform Design Info for Affymetrix Mapping50K_Hind240") + (description "This package provides platform design info for Affymetrix +Mapping50K_Hind240.") + (license license:artistic2.0))) + (define-public r-pd-mapping50k-xba240 (package (name "r-pd-mapping50k-xba240") @@ -390,17 +665,38 @@ Database}.") Mapping50K_Xba240 (pd.mapping50k.xba240).") (license license:artistic2.0))) +(define-public r-polyphen-hsapiens-dbsnp131 + (package + (name "r-polyphen-hsapiens-dbsnp131") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "PolyPhen.Hsapiens.dbSNP131" version + 'annotation)) + (sha256 + (base32 "1kikygkli41sn3rqihz0924prmqg2264ifj29vmg1a7qccm0kf7c")))) + (properties `((upstream-name . "PolyPhen.Hsapiens.dbSNP131"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-rsqlite r-variantannotation)) + (home-page "https://bioconductor.org/packages/PolyPhen.Hsapiens.dbSNP131") + (synopsis "PolyPhen predictions for Homo sapiens dbSNP build 131") + (description + "This package provides a database of @code{PolyPhen} predictions for Homo +sapiens @code{dbSNP} build 131.") + (license license:artistic2.0))) + (define-public r-reactome-db (package (name "r-reactome-db") - (version "1.88.0") + (version "1.89.0") (source (origin (method url-fetch) (uri (bioconductor-uri "reactome.db" version 'annotation)) (sha256 (base32 - "1fwbf53vklhvqa6n6pijb8xqyv2pap1hskkirnm5c42wmd6g4ql7")))) + "1r4h9wdm3h99b9w18kihma8n9hprxqp1il5k43cfrf191l6wic38")))) (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs @@ -412,6 +708,27 @@ Mapping50K_Xba240 (pd.mapping50k.xba240).") database, assembled using data from REACTOME.") (license license:cc-by4.0))) +(define-public r-sift-hsapiens-dbsnp137 + (package + (name "r-sift-hsapiens-dbsnp137") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SIFT.Hsapiens.dbSNP137" version + 'annotation)) + (sha256 + (base32 "1472abqanbwziyynr851xzhg7ck8w1n98ymmggg7s46hzix5mlj8")))) + (properties `((upstream-name . "SIFT.Hsapiens.dbSNP137"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-rsqlite r-variantannotation)) + (home-page "https://bioconductor.org/packages/SIFT.Hsapiens.dbSNP137") + (synopsis "PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137") + (description + "This package provides a database of PROVEAN/SIFT predictions for Homo +sapiens @code{dbSNP} build 137.") + (license license:artistic2.0))) + (define-public r-bsgenome-btaurus-ucsc-bostau8 (package (name "r-bsgenome-btaurus-ucsc-bostau8") @@ -766,13 +1083,13 @@ in Biostrings objects.") (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") - (version "1.2.12") + (version "1.2.13") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation)) (sha256 (base32 - "0md3jl5bz4d2wkvf4yra7rydf5dgykrijrdqwwxc7f77l30nsmgp")))) + "0kh7yxk8aqadv9xdnvrp2ysa1xxxgjqkj83w3bw1w9k55r1kr8si")))) (properties `((upstream-name . "GenomeInfoDbData"))) (build-system r-build-system) @@ -785,13 +1102,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-go-db (package (name "r-go-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GO.db" version 'annotation)) (sha256 (base32 - "199vk4y069yik7fn25pp73nkhs1vaw9km9rcmm1cirncwm2n0vhg")))) + "1p0hw5j6a7q7pgp7l40rs27ci16n6jpyd39irhrpys94hqrqx5pz")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) @@ -807,19 +1124,19 @@ information about the latest version of the Gene Ontologies.") (define-public r-hdo-db (package (name "r-hdo-db") - (version "0.99.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDO.db" version 'annotation)) (sha256 (base32 - "14ngyxailmxrbxqqi9m7mchqcvchmbg7zm34i8a927b20s6z4z61")))) + "0h026xkncm8nc1q8z7qk3nlw445rf3dncaf20b80x7xfl2nm3f84")))) (properties `((upstream-name . "HDO.db"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi)) + (list r-annotationdbi r-dbi)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/HDO.db") (synopsis "Annotation maps describing the entire Human Disease Ontology") (description @@ -843,12 +1160,12 @@ https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}. `((upstream-name . "Homo.sapiens"))) (build-system r-build-system) (propagated-inputs - (list r-genomicfeatures + (list r-annotationdbi + r-genomicfeatures r-go-db r-org-hs-eg-db - r-txdb-hsapiens-ucsc-hg19-knowngene r-organismdbi - r-annotationdbi)) + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/Homo.sapiens/") (synopsis "Annotation package for the Homo.sapiens object") (description @@ -953,21 +1270,48 @@ data.") "This is an annotation package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +(define-public r-illuminahumanmethylationepicv2anno-20a1-hg38 + (package + (name "r-illuminahumanmethylationepicv2anno-20a1-hg38") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "IlluminaHumanMethylationEPICv2anno.20a1.hg38" + version + 'annotation)) + (sha256 + (base32 "0vp4m3a7qal4d8qc9xaj7z3x484i33ix4c67qlbw0kskdir7rq5a")))) + (properties `((upstream-name . "IlluminaHumanMethylationEPICv2anno.20a1.hg38"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (native-inputs (list r-knitr)) + (home-page + "https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html") + (synopsis "Annotation for Illumina's EPIC v2.0 methylation arrays") + (description + "This is an annotation package for Illumina's EPIC v2.0 methylation +arrays. The version 2 covers more than 935K CpG sites in the human genome +hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K +methylation array).") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) (sha256 (base32 - "0vg6nw4qzj8janmkv6k2z471m3l4xnd1h232h0w5i53b20c7p6ys")))) + "1r7fzzrqcas23bxcd55ppflx0ls1biifis3qj36iv5gwhhwimq3i")))) (properties `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") (synopsis "Genome wide annotation for Worm") (description @@ -978,18 +1322,19 @@ annotations for the genome of the model worm Caenorhabditis elegans.") (define-public r-org-dm-eg-db (package (name "r-org-dm-eg-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) (sha256 (base32 - "1sqw38z73sgq66x8qrb5xw0jxyimy7l1hs2iwm7xq9ylzrjw3yj0")))) + "1v21rx7kpdi30898jbnvg1cd3xgghvqhkiipkasn5wjz22z1lqna")))) (properties `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") (synopsis "Genome wide annotation for Fly") (description @@ -1000,18 +1345,19 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") (define-public r-org-dr-eg-db (package (name "r-org-dr-eg-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) (sha256 (base32 - "041hp3xhkiwh8vb4zq5kwvrsmp8paqlri6gaj1qy0a5zjlkw0fl6")))) + "0ayva6p2qav16s4nvngxqi8zwl4ylrl5riww3lwc2dql0kkgbvrs")))) (properties `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") (synopsis "Annotation for Zebrafish") (description @@ -1022,18 +1368,19 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) (sha256 (base32 - "1xrbf0zmik1j70i6bg5wqvfwz4vcf3vgypan36r1lv6lspsfychr")))) + "1gykdrfkzvx83bkpbggsnk8gd0w9xh5g071r3ngykjh5x36w6dlc")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") (synopsis "Genome wide annotation for Human") (description @@ -1044,18 +1391,19 @@ on mapping using Entrez Gene identifiers.") (define-public r-org-mm-eg-db (package (name "r-org-mm-eg-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) (sha256 (base32 - "12d8lrf6bxvqzfxzdbxqmjcywy2myhwhi99kxdwpijsczxxfikj7")))) + "1wlc34qq0hv9fmdw810jc26gyf7ibicy8rsbll4is7bp2i1hxk47")))) (properties `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) + (native-inputs (list r-runit)) (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") (synopsis "Genome wide annotation for Mouse") (description @@ -1173,15 +1521,23 @@ Ensembl.") (define-public r-escape (package (name "r-escape") - (version "2.0.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "escape" version)) (sha256 - (base32 "03wbrxd7kjyl3d4s418ql5fv7bmwdfyfp10jd8knr0xis7vxmz2x")))) + (base32 "0874r80za3kxf9vc9arz8ncsddqffzi6a28vivaah293kg23nc0m")))) (properties `((upstream-name . "escape"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This one test fails with accuracy errors. + (delete-file "tests/testthat/test-performPCA.R")))))) (propagated-inputs (list r-aucell r-biocparallel r-dplyr @@ -1191,6 +1547,7 @@ Ensembl.") r-ggridges r-gseabase r-gsva + r-matrix r-matrixgenerics r-msigdbr r-patchwork @@ -1200,7 +1557,7 @@ Ensembl.") r-stringr r-summarizedexperiment r-ucell)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-seurat r-testthat)) (home-page "https://bioconductor.org/packages/escape") (synopsis "Single cell analysis platform for enrichment") (description @@ -1210,6 +1567,27 @@ sequencing. Using raw count information, Seurat objects, or across individual cells.") (license license:gpl2))) +(define-public r-sift-hsapiens-dbsnp132 + (package + (name "r-sift-hsapiens-dbsnp132") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SIFT.Hsapiens.dbSNP132" version + 'annotation)) + (sha256 + (base32 "1akqhmv9hp41q2jrvz4xvpdi30c4c6v4xbz6ykn6pdf0217p7xry")))) + (properties `((upstream-name . "SIFT.Hsapiens.dbSNP132"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-rsqlite r-variantannotation)) + (home-page "https://bioconductor.org/packages/SIFT.Hsapiens.dbSNP132") + (synopsis "SIFT Predictions for Homo sapiens dbSNP build 132") + (description + "This package provides a database of SIFT predictions for Homo sapiens +@code{dbSNP} build 132.") + (license license:artistic2.0))) + (define-public r-snplocs-hsapiens-dbsnp144-grch37 (package (name "r-snplocs-hsapiens-dbsnp144-grch37") @@ -1227,12 +1605,11 @@ across individual cells.") (arguments `(#:substitutable? #f)) (propagated-inputs (list r-biocgenerics - r-s4vectors - r-iranges + r-bsgenome r-genomeinfodb r-genomicranges - r-bsgenome - r-biostrings)) + r-iranges + r-s4vectors)) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") @@ -1288,7 +1665,7 @@ exposing these as TxDb objects.") `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) (propagated-inputs - (list r-genomicfeatures)) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -1301,13 +1678,13 @@ track. The database is exposed as a @code{TxDb} object.") (define-public r-txdb-hsapiens-ucsc-hg38-knowngene (package (name "r-txdb-hsapiens-ucsc-hg38-knowngene") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" version 'annotation)) (sha256 - (base32 "0ak6acjll2djamakpn60ks47lfs2y0r8xwhjazj6fvch34xkc2d5")))) + (base32 "15qmd51wcjhwzg3w1s13ky39km0waypwzipvr4cisvhvkbr7sqn4")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) @@ -1337,7 +1714,7 @@ track. The database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) (build-system r-build-system) (propagated-inputs - (list r-genomicfeatures r-annotationdbi)) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") (synopsis "Annotation package for mouse genome in TxDb format") @@ -1347,6 +1724,28 @@ is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) +(define-public r-txdb-mmusculus-ucsc-mm10-ensgene + (package + (name "r-txdb-mmusculus-ucsc-mm10-ensgene") + (version "3.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.ensGene" version + 'annotation)) + (sha256 + (base32 "0saxi1fdiwd38sfvy1rynd3v44rbp158jv6sjqcivvaqnd84zg9s")))) + (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.ensGene"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi r-genomicfeatures)) + (home-page + "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.ensGene") + (synopsis "Annotation package for TxDb object(s)") + (description + "This package exposes an annotation databases generated from UCSC by +exposing these as @code{TxDb} objects.") + (license license:artistic2.0))) + (define-public r-txdb-mmusculus-ucsc-mm10-knowngene (package (name "r-txdb-mmusculus-ucsc-mm10-knowngene") @@ -1362,7 +1761,7 @@ database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) (propagated-inputs - (list r-bsgenome r-genomicfeatures r-annotationdbi)) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") @@ -1412,7 +1811,7 @@ by exposing these as TxDb objects.") `((upstream-name . "FDb.InfiniumMethylation.hg19"))) (build-system r-build-system) (propagated-inputs - (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db + (list r-annotationdbi r-biostrings r-genomicfeatures r-org-hs-eg-db r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") @@ -1444,6 +1843,31 @@ annotations.") "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +(define-public r-illuminahumanmethylationepicv2manifest + (package + (name "r-illuminahumanmethylationepicv2manifest") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "IlluminaHumanMethylationEPICv2manifest" + version 'annotation)) + (sha256 + (base32 "1z4b15x8cai27cqhl2lhl02nx0lv8q5c1774vdvvdajx2hivn77l")))) + (properties `((upstream-name . "IlluminaHumanMethylationEPICv2manifest"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (native-inputs (list r-knitr)) + (home-page + "https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html") + (synopsis "Manifest for Illumina's EPIC v2.0 methylation arrays") + (description + "This package provides a manifest package for Illumina's EPIC v2.0 +methylation arrays. The version 2 covers more than 935K CpG sites in the +human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the +850K methylation array).") + (license license:artistic2.0))) + (define-public r-do-db (package (name "r-do-db") @@ -1479,6 +1903,7 @@ Disease Ontology.") (properties `((upstream-name . "hgu133plus2.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/hgu133plus2.db") (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data") (description @@ -1489,13 +1914,13 @@ data (chip hgu133plus2) assembled using data from public repositories.") (define-public r-pfam-db (package (name "r-pfam-db") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PFAM.db" version 'annotation)) (sha256 - (base32 "0jjba22p8x4cfnihsa3gah3amdr4yrqpfm0zfr990jcjkvf94wvk")))) + (base32 "0ibhdvb7vc2s70n6dq13357y9fgvkg0bdjxcq13n9rqajk6bmaw6")))) (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs @@ -1576,12 +2001,12 @@ All datasets are restricted to protein coding genes.") (define-public r-adductdata (package (name "r-adductdata") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductData" version 'experiment)) (sha256 - (base32 "1ydd7zxag0cmw7mj38srqs4w6lbp1ic5i8s1ay6pifv14arcncrz")))) + (base32 "1s9vflcvsi1136ax0isc1zskbz64cis6mlhhd458jrsx34cf5hff")))) (properties `((upstream-name . "adductData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-experimenthub)) @@ -1594,15 +2019,46 @@ of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum albumin} (HSA).") (license license:artistic2.0))) +(define-public r-airway + (package + (name "r-airway") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "airway" version + 'experiment)) + (sha256 + (base32 "0cj8s2pxydq7n644lf07vb9g89gqbd91s3m0d0x1qvbp1sskp536")))) + (properties `((upstream-name . "airway"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/airway") + (synopsis + "RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells") + (description + "This package provides a @code{RangedSummarizedExperiment} object of read +counts in genes for an RNA-Seq experiment on four human airway smooth muscle +cell lines treated with dexamethasone. Details on the gene model and read +counting procedure are provided in the package vignette. The citation for the +experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, +Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R +Jr, Tantisira KG, Weiss ST, Lu Q. RNA-Seq Transcriptome Profiling Identifies +CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function +in Airway Smooth Muscle Cells. P@code{LoS} One. 2014 Jun 13;9(6):e99625. +PMID: 24926665. GEO: GSE52778.") + (license license:lgpl2.0+))) + (define-public r-aneufinderdata (package (name "r-aneufinderdata") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinderData" version 'experiment)) (sha256 - (base32 "1qysi874hsa4a7xz0na0cxv0sx02d3b74h77s30mfww1wsg8jy69")))) + (base32 "039ymqwxr66hmkzig333gwjxczzxlc6jl1x27jw7agriynjbqmgx")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/AneuFinderData/") (synopsis "Data package for @code{AneuFinder}") @@ -1613,12 +2069,12 @@ demonstration purposes in the @code{AneuFinder} package.") (define-public r-arrmdata (package (name "r-arrmdata") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmData" version 'experiment)) (sha256 - (base32 "02y44d0dappc3srl2d7lgipm6a62gvd8vivzaq4594dnmy8rvkw3")))) + (base32 "0hic3rm9z1z98dqg6g7nvs4mdq7xn0xvkpraqv95zw1izs0zvndi")))) (properties `((upstream-name . "ARRmData"))) (build-system r-build-system) @@ -1632,14 +2088,14 @@ from Illumina 450k methylation arrays.") (define-public r-bcellviper (package (name "r-bcellviper") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bcellViper" version 'experiment)) (sha256 (base32 - "0mx92gs9065lz0c01mzng9snalvmdb3xbsm1r3f6fnhg478da4yq")))) + "140wwk0d3lds60x7b0w2612ss0bdlbjza351j1w576bda47a48rg")))) (properties `((upstream-name . "bcellViper"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -1652,17 +2108,40 @@ regulatory network. In addition, this package provides a human normal B-cells dataset for the examples in package viper.") (license license:gpl2+))) +(define-public r-biotmledata + (package + (name "r-biotmledata") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biotmleData" version + 'experiment)) + (sha256 + (base32 "0bnjhn0xirv81lw83ymd4mcmllkrd19gya7fr4j7xq77hjrx1kl7")))) + (properties `((upstream-name . "biotmleData"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/biotmleData") + (synopsis + "Example experimental microarray data set for the \"biotmle\" R package") + (description + "This package provides microarray data (from the Illumina Ref-8 BeadChips +platform) and phenotype-level data from an epidemiological investigation of +benzene exposure, packaged using @code{SummarizedExperiemnt}, for use as an +example with the @code{biotmle} R package.") + (license license:expat))) + (define-public r-bladderbatch (package (name "r-bladderbatch") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bladderbatch" version 'experiment)) (sha256 (base32 - "00cgkpa6mb32q3xl5clkpdh5rkwx7c81rxmyh2qr0jpwpmd3gjwc")))) + "14lik0n2b3fnvggrcash3kcd03vgzqimzhv9w3vagz0cbvdr0s01")))) (properties `((upstream-name . "bladderbatch"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -1676,18 +2155,20 @@ dataset for the examples in package viper.") (define-public r-bodymaprat (package (name "r-bodymaprat") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bodymapRat" version 'experiment)) (sha256 - (base32 "15kjgqq7lq94pjqg380swqrkv684kgbpkaikfxxdx4cpgx8sjzn7")))) + (base32 "06rqhnri8nwy1p8srzmhi0z81q9nwdk1q413if7n3760gp0qfgbn")))) (properties `((upstream-name . "bodymapRat"))) (build-system r-build-system) (arguments (list + ;; Tests fail with: could not find function "bodymapRat" + #:tests? #false #:phases '(modify-phases %standard-phases (add-after 'unpack 'set-HOME @@ -1701,7 +2182,7 @@ dataset for the examples in package viper.") (string-append "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}")))))))) (propagated-inputs (list r-experimenthub r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/bodymapRat") (synopsis "Experimental dataset from the rat BodyMap project") (description @@ -1714,13 +2195,13 @@ STAR. Data is available on @code{ExperimentHub} as a data package.") (define-public r-biscuiteerdata (package (name "r-biscuiteerdata") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteerData" version 'experiment)) (sha256 - (base32 "1qv2ajy312diacb3mihc3q7hrrlq48k5vd9v0g6w38cqz6gnz0as")))) + (base32 "0x80ccnlh6wdknxfrkj8y6lxx2b369ma7hc9znhzw2xgr9fj6qpm")))) (properties `((upstream-name . "biscuiteerData"))) (build-system r-build-system) @@ -1737,13 +2218,13 @@ biscuiteer.") (define-public r-breakpointrdata (package (name "r-breakpointrdata") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breakpointRdata" version 'experiment)) (sha256 (base32 - "1hm190ji3s451x2hchmpyzx6v4n8p1n6fdqg7cbzmj19rzsb4wha")))) + "08kwslm55w0vmcdjndsaq51pwm8gvlrxqy9cjz87dmwxd42giv46")))) (properties `((upstream-name . "breakpointRdata"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1757,14 +2238,14 @@ demonstrate functionalities of the @code{breakpointR} package.") (define-public r-breastcancervdx (package (name "r-breastcancervdx") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breastCancerVDX" version 'experiment)) (sha256 - (base32 "0mvm2a77mss85vi8x3i35d54z70advyshsmadhl6aysrzfiw5ifd")))) + (base32 "1q248675kn2r0q7spw6wa8fhcihsk98diys3zfr36xba1pr3f8yy")))) (properties `((upstream-name . "breastCancerVDX"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/breastCancerVDX") @@ -1777,15 +2258,17 @@ cancer study published in Wang et al. 2005 and Minn et al 2007.") (define-public r-celldex (package (name "r-celldex") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "celldex" version 'experiment)) (sha256 - (base32 "155hnh62ra06b52xk78f111b10gm34d1djvl5w5mabvrk4vknwj6")))) + (base32 "0kn1mdnbiiag29n52gar2ymihx5q9hrjfjc6qssxm0m7ns9gm4hm")))) (properties `((upstream-name . "celldex"))) (build-system r-build-system) + ;; Tests access the internet via r-gypsum. + (arguments (list #:tests? #false)) (propagated-inputs (list r-alabaster-base r-alabaster-matrix @@ -1802,7 +2285,7 @@ cancer study published in Wang et al. 2005 and Minn et al 2007.") r-rsqlite r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/LTLA/celldex") (synopsis "Reference index for cell types") (description @@ -1814,13 +2297,13 @@ single-cell data or deconvolution of bulk RNA-seq.") (define-public r-champdata (package (name "r-champdata") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChAMPdata" version 'experiment)) (sha256 (base32 - "0x006ilgqrf15135ivxv8qrcyhssl1w6pm1gpnna96za58l2f2rr")))) + "0gcd58ad61niknq1dqn8ydr4v31i718jcg75q1hklbn78xlj2m3f")))) (properties `((upstream-name . "ChAMPdata"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-genomicranges)) @@ -1831,16 +2314,38 @@ single-cell data or deconvolution of bulk RNA-seq.") and blood controls for CNA analysis.") (license license:gpl3))) +(define-public r-chipexoqualexample + (package + (name "r-chipexoqualexample") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPexoQualExample" version + 'experiment)) + (sha256 + (base32 "0c6lxl79j65pqy6sgnwaqz83r9fwh0m10xmnj9zcp8s0j1cxn5xq")))) + (properties `((upstream-name . "ChIPexoQualExample"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://www.github.com/keleslab/ChIPexoQualExample") + (synopsis "Example data for the ChIPexoQual package") + (description + "This package contains data for the @code{ChIPexoQual} package, +consisting of 3 chromosome 1 aligned reads from a @code{ChIP-exo} experiment +for @code{FoxA1} in mouse liver cell lines aligned to the mm9 genome.") + (license license:gpl2+))) + (define-public r-chromstardata (package (name "r-chromstardata") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaRData" version 'experiment)) (sha256 - (base32 "0v28zg8z5b72hci7rqbvjvcgp979zxnq6xgck4baypmkj9ac5wn3")))) + (base32 "19kb4ya8p5shhm2zcdf8y172w8fsg409fjmkqlyagpncvcak0b04")))) (properties `((upstream-name . "chromstaRData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/chromstaRData/") @@ -1853,13 +2358,13 @@ chromstaR package.") (define-public r-copyhelper (package (name "r-copyhelper") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) (sha256 - (base32 "1ijlba601wknkj6ybbnarcdw1z54f76gkdgynpry1v8jpbpvcadr")))) + (base32 "1zg2cp7rff6yc1lk70gipy0q3z6ndizipay3102psv1q2916x8ln")))) (properties `((upstream-name . "CopyhelpeR"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/CopyhelpeR/") @@ -1873,17 +2378,63 @@ display copy number variation. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.") (license license:gpl2))) +(define-public r-derfinderdata + (package + (name "r-derfinderdata") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "derfinderData" version + 'experiment)) + (sha256 + (base32 "0rkc54gh3yasms4nrayi58ly2raad0ksid3wmzbmhy22zib4n9hy")))) + (properties `((upstream-name . "derfinderData"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/leekgroup/derfinderData") + (synopsis "Processed BigWigs from BrainSpan for examples") + (description + "This package provides processed 22 samples from @code{BrainSpan} keeping +only the information for chromosome 21. Data is stored in the @code{BigWig} +format and is used for examples in other packages.") + (license license:artistic2.0))) + +(define-public r-faahko + (package + (name "r-faahko") + (version "1.46.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "faahKO" version + 'experiment)) + (sha256 + (base32 "1i52f5anjvag3n6hn1w6wyjc81h81rfb5a7w1lcnkg4q87g149nm")))) + (properties `((upstream-name . "faahKO"))) + (build-system r-build-system) + (propagated-inputs (list r-xcms)) + (home-page "http://dx.doi.org/10.1021/bi0480335") + (synopsis "Saghatelian et al. (2004) FAAH knockout LC/MS data") + (description + "This package includes positive ionization mode data in @code{NetCDF} +file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data +originally reported in \"Assignment of Endogenous Substrates to Enzymes by +Global Metabolite Profiling\" Biochemistry; 2004; 43(45). It also includes +detected peaks in an @code{xcmsSet}.") + (license license:lgpl2.0+))) + (define-public r-flowsorted-blood-450k (package (name "r-flowsorted-blood-450k") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSorted.Blood.450k" version 'experiment)) (sha256 (base32 - "0lc45dg5jq0kqycpsggrhi5fa4xj1ciqrj6iw548ccjgdyy2w1xh")))) + "1afjwjddx9nwg01png223zr9vcb3xq8i71wx8mj2cxdwsb0lyqsq")))) (properties `((upstream-name . "FlowSorted.Blood.450k"))) (build-system r-build-system) (propagated-inputs (list r-minfi)) @@ -1899,14 +2450,14 @@ associated with cell type.") (define-public r-flowsorted-blood-epic (package (name "r-flowsorted-blood-epic") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSorted.Blood.EPIC" version 'experiment)) (sha256 (base32 - "1b0azyslk2g08i6v1vv2niw32f0zqasw85b9klw83zdy2f5dcdvh")))) + "1zq5xbgr4r68mmzsszb16w11axkmgrxcrpl56dy33szs0ahk10xs")))) (properties `((upstream-name . "FlowSorted.Blood.EPIC"))) (build-system r-build-system) (propagated-inputs @@ -1918,7 +2469,7 @@ associated with cell type.") r-quadprog r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/immunomethylomics/FlowSorted.Blood.EPIC") (synopsis "Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells") @@ -1930,16 +2481,39 @@ Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.") (license license:gpl3))) +(define-public r-flowworkspacedata + (package + (name "r-flowworkspacedata") + (version "3.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowWorkspaceData" version + 'experiment)) + (sha256 + (base32 "1bwykpv1y76iq0qhnn24snwymy0wirip7xwq1wqj1flbainzmv6g")))) + (properties `((upstream-name . "flowWorkspaceData"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/flowWorkspaceData") + (synopsis "Data for flowWorkspace tests and vignettes") + (description + "The necessary external data to run the @code{flowWorkspace} and +@code{openCyto} vignette is found in this package. This data package contains +two flowJo, one diva xml workspace and the associated @code{fcs} files as well +as three @code{GatingSets} for testing the @code{flowWorkspace}, +@code{openCyto} and @code{CytoML} packages.") + (license license:gpl2))) + (define-public r-genelendatabase (package (name "r-genelendatabase") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) (sha256 - (base32 "0c8f0sqgrg7rc2vs9id9xzbwwv3zhy6ylqiisji20rw9ipzgv7k8")))) + (base32 "1v23v859w75svl2vl0758h8i41mjy5vq6xq4w6z8v8w3zyhwycgp")))) (properties `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) @@ -1955,13 +2529,13 @@ genomes and gene ID formats, largely based on the UCSC table browser.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomationData" version 'experiment)) (sha256 - (base32 "16mghhik2xzin14d7mqlwfy2dah3ccnga947z9id44vyz906wws7")))) + (base32 "1ml8p99y4lba2gzphf0hsy840yqvfsanqscjh7sww5gk06yx9c4p")))) (properties `((upstream-name . "genomationData"))) (build-system r-build-system) @@ -1978,16 +2552,65 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-golubesets + (package + (name "r-golubesets") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "golubEsets" version + 'experiment)) + (sha256 + (base32 "0f0lk9qp6d5frvgs5c34jm7fhnjw4v76wi45pdjbh0sr0fhzxf9z")))) + (properties `((upstream-name . "golubEsets"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/golubEsets") + (synopsis "ExpressionSets for golub leukemia data") + (description + "This is a representation of public golub data with some covariate data +of provenance unknown to the maintainer at present; it now employs +@code{ExpressionSet} format.") + (license license:lgpl2.0+))) + +(define-public r-gsvadata + (package + (name "r-gsvadata") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GSVAdata" version + 'experiment)) + (sha256 + (base32 "160k1vsxcbjqwpfkdkhd7dsvnaasjbs270gnfdwdbnl0c6d24348")))) + (properties `((upstream-name . "GSVAdata"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-gseabase r-hgu95a-db + r-summarizedexperiment)) + (home-page "https://bioconductor.org/packages/GSVAdata") + (synopsis "Data employed in the vignette of the GSVA package") + (description + "This package stores the data employed in the vignette of the GSVA package. +These data belong to the following publications: Armstrong et al. Nat Genet +30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, +Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et +al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak +et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331, +2021.") + (license license:artistic2.0))) + (define-public r-hdcytodata (package (name "r-hdcytodata") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDCytoData" version 'experiment)) (sha256 (base32 - "0pmzgp7x1zam3b7agi8mdq14qmx8nln9lnhiglax2pvg2a5n4ii4")))) + "10b5fjhyrz5rm08xrniv6pnnay0h96bhs838napxsmjgvmhqbibn")))) (properties `((upstream-name . "HDCytoData"))) (build-system r-build-system) (arguments @@ -2022,14 +2645,14 @@ includes channel names, protein marker names, and protein marker classes.") (define-public r-illumina450probevariants-db (package (name "r-illumina450probevariants-db") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Illumina450ProbeVariants.db" version 'experiment)) (sha256 (base32 - "1jpknhp624753rhalf81kvl02k4wj19xpncagzf85c878953vph0")))) + "0sp9znznmqhf0h4g5gbz34hn3frki6nfqvfs7v1w6kin3y9k2gr5")))) (properties `((upstream-name . "Illumina450ProbeVariants.db"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/Illumina450ProbeVariants.db") @@ -2041,16 +2664,36 @@ bead chip for each of the four populations (Asian, American, African and European).") (license license:gpl3))) +(define-public r-illuminadatatestfiles + (package + (name "r-illuminadatatestfiles") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "IlluminaDataTestFiles" version + 'experiment)) + (sha256 + (base32 "0xwck8i2r2866kaimwy9klg85fs81f6h4i9zw20zxxd0qmqkpzwi")))) + (properties `((upstream-name . "IlluminaDataTestFiles"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/IlluminaDataTestFiles") + (synopsis "Illumina microarray files (IDAT) for testing") + (description + "This package contains example data for Illumina microarray output files, +for testing purposes.") + (license license:artistic2.0))) + (define-public r-italicsdata (package (name "r-italicsdata") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICSData" version 'experiment)) (sha256 - (base32 "1d0awis142kgx9hi0dggl6gqg17m0awqzn8ncpqh2lwaka372dq8")))) + (base32 "0gdr3r7ivyyfawrx5bmlqf617z3s3hcv4la58bd0wq9xdw79fw74")))) (properties `((upstream-name . "ITALICSData"))) (build-system r-build-system) (home-page "http://bioinfo.curie.fr") @@ -2063,13 +2706,13 @@ package.") (define-public r-jaspar2016 (package (name "r-jaspar2016") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "JASPAR2016" version 'experiment)) (sha256 - (base32 "09q5m71drbp64n26plr0a9bz71akcs4g7pqqyjmsmjrzi40kx7hr")))) + (base32 "0vg47zvpb20vhk177d1hj959cj1srfql10ywakzkhw7h4hmc8jnl")))) (properties `((upstream-name . "JASPAR2016"))) (build-system r-build-system) (home-page "https://jaspar.elixir.no/") @@ -2079,17 +2722,61 @@ package.") please use the package TFBSTools.") (license license:gpl2))) +(define-public r-leukemiaseset + (package + (name "r-leukemiaseset") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "leukemiasEset" version 'experiment)) + (sha256 + (base32 "1zgzg38l24vf27hhyywiv5gan6n25idziwxva09nc5qw4hyy8ikr")))) + (properties `((upstream-name . "leukemiasEset"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/leukemiasEset") + (synopsis "Leukemia's microarray gene expression data (expressionSet)") + (description + "This package provides an @code{expressionSet} containing gene expression +data from 60 bone marrow samples of patients with one of the four main types +of leukemia (ALL, AML, CLL, CML) or non-leukemia.") + (license license:gpl2+))) + +(define-public r-lungcancerlines + (package + (name "r-lungcancerlines") + (version "0.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "LungCancerLines" version + 'experiment)) + (sha256 + (base32 "1g6h8b94hrn8wp6fhjwx1mkrdmqmpmp1y22979apf4fn2al10y17")))) + (properties `((upstream-name . "LungCancerLines"))) + (build-system r-build-system) + (propagated-inputs (list r-rsamtools)) + (home-page "https://bioconductor.org/packages/LungCancerLines") + (synopsis "Reads from Two Lung Cancer Cell Lines") + (description + "This package contains reads from an RNA-seq experiment between two lung +cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as +Fastq files and are meant for use with the TP53Genome object in the +@code{gmapR} package.") + (license license:artistic2.0))) + (define-public r-macrophage (package (name "r-macrophage") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "macrophage" version 'experiment)) (sha256 (base32 - "11ydl4srfxbcqnb42kwk783xd74231g6vgp1f0qs3hl8slc1hk1w")))) + "0dw15l1zs1byk9afhf7rlh9pifvn356slm5l4pagcfhn867qd5d6")))) (properties `((upstream-name . "macrophage"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2150,17 +2837,41 @@ motif lists, and novel data visualizations. Memes functions and data structures are amenable to both base R and tidyverse workflows.") (license license:expat)))) +(define-public r-methylaiddata + (package + (name "r-methylaiddata") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MethylAidData" version + 'experiment)) + (sha256 + (base32 "1y8kcbbi76cfw379g2wlml2adkf0vn1bmyhqq8vp70vdc23n9vr1")))) + (properties `((upstream-name . "MethylAidData"))) + (build-system r-build-system) + (propagated-inputs (list r-methylaid)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MethylAidData") + (synopsis + "MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples") + (description + "This package provides a data package containing summarized Illumina 450k +array data on 2800 samples and summarized EPIC data for 2620 samples. The +data can be use as a background data set in the interactive application.") + (license license:gpl2+))) + (define-public r-methylclockdata (package (name "r-methylclockdata") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylclockData" version 'experiment)) (sha256 - (base32 "1bwrgib7k71i4i6iq4l71n0z9adq3bg9k8j10bpi79ygn9169np5")))) + (base32 "1ivl919xlrdqi1y1y4i5793925vd2ysj582wr9r4kwnird2dwbmw")))) (properties `((upstream-name . "methylclockData"))) (build-system r-build-system) (propagated-inputs (list r-experimenthub r-experimenthubdata)) @@ -2181,14 +2892,14 @@ with different methylation clocks.") (define-public r-mousegastrulationdata (package (name "r-mousegastrulationdata") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MouseGastrulationData" version 'experiment)) (sha256 (base32 - "0adw98vym1jir1jrzaws7zrlfvls6rfl8bvkpq5sjy4crb33lxy2")))) + "1w2907hcja7rkdrizh0rmdf75liy2zx4v9kxp4xx12x222q9ngz6")))) (properties `((upstream-name . "MouseGastrulationData"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -2198,7 +2909,7 @@ with different methylation clocks.") r-singlecellexperiment r-spatialexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/MarioniLab/MouseGastrulationData") (synopsis "Single-Cell omics data across mouse gastrulation and early organogenesis") @@ -2212,13 +2923,13 @@ timecourse of mouse gastrulation and early organogenesis.") (define-public r-minfidata (package (name "r-minfidata") - (version "0.50.0") + (version "0.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfiData" version 'experiment)) (sha256 (base32 - "1myxv7cqh7d1rjav9qhwqsmw3s1xh3zm34vbxwprqaqg87dg4bw0")))) + "0vhf8hknls4dw49jgbgxqd8znx474g7x3imzvsh43cb7cs89xj3i")))) (properties `((upstream-name . "minfiData"))) (build-system r-build-system) (propagated-inputs @@ -2232,16 +2943,61 @@ timecourse of mouse gastrulation and early organogenesis.") methylation arrays.") (license license:artistic2.0))) +(define-public r-minfidataepic + (package + (name "r-minfidataepic") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "minfiDataEPIC" version + 'experiment)) + (sha256 + (base32 "0xqciawmlfxcb0s60d0dk9mc9jga12dmm7qx3dqs1i6p69lmdbiy")))) + (properties `((upstream-name . "minfiDataEPIC"))) + (build-system r-build-system) + (propagated-inputs (list r-illuminahumanmethylationepicanno-ilm10b2-hg19 + r-illuminahumanmethylationepicmanifest r-minfi)) + (home-page "https://bioconductor.org/packages/minfiDataEPIC") + (synopsis "Example data for the Illumina Methylation EPIC array") + (description + "This package provides data from 3 technical replicates of the cell line +GM12878 from the EPIC methylation array.") + (license license:artistic2.0))) + +(define-public r-minionsummarydata + (package + (name "r-minionsummarydata") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "minionSummaryData" version + 'experiment)) + (sha256 + (base32 "0x5d0wrl6ck12g5xq8flyngvwi2wvij9pb6km34g7rz1c34wjj1n")))) + (properties `((upstream-name . "minionSummaryData"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/minionSummaryData") + (synopsis + "Summarized MinION sequencing data published by Ashton et al. 2015") + (description + "This package provides summarized @code{MinION} sequencing data for +Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are +each provided as @code{Fast5Summary} objects.") + (license license:expat))) + (define-public r-msdata (package (name "r-msdata") - (version "0.44.0") + (version "0.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msdata" version 'experiment)) (sha256 - (base32 "0g7mlgks3nfnfipnybs7pvsnmrvmq8888g39badca8pi73q1cm25")))) + (base32 "10b8anw0ygbsq95p89agjhs3qvgj9xrlrblg75cdbgmlzks2jhdl")))) (properties `((upstream-name . "msdata"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/msdata") @@ -2258,14 +3014,16 @@ files for various search engines.") (define-public r-msexperiment (package (name "r-msexperiment") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsExperiment" version)) (sha256 - (base32 "0dxv3jw5aj1i73vqrp3c031pj26i7rp0q2zs4nq3x1vni349506d")))) - (properties `((upstream-name . "MsExperiment"))) + (base32 "15vxwvgimliyzj0rb06s7rpm3wrz3gc1n0wdgs0jd4flwp152g9h")))) + (properties + `((upstream-name . "MsExperiment") + (updater-extra-native-inputs . ("r-mzr")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-dbi @@ -2275,7 +3033,15 @@ files for various search engines.") r-s4vectors r-spectra r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr + r-msbackendsql + r-msdata + r-mzr + r-rsqlite + r-s4vectors + r-spectra + r-summarizedexperiment + r-testthat)) (home-page "https://github.com/RforMassSpectrometry/MsExperiment") (synopsis "Infrastructure for Mass Spectrometry experiments") (description @@ -2294,14 +3060,14 @@ containers.") (define-public r-msigdb (package (name "r-msigdb") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msigdb" version 'experiment)) (sha256 (base32 - "080wm9sjwqhaxqx1r3kly1bi1gvkssqpsadnvabx11w493356qr0")))) + "1bla3jj5vdvb956pz07fxsihiwqlkpm409rdhljbdnld438q3kpp")))) (properties `((upstream-name . "msigdb"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -2310,7 +3076,7 @@ containers.") r-gseabase r-org-hs-eg-db r-org-mm-eg-db)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://doi.org/doi:10.18129/B9.bioc.msigdb") (synopsis "ExperimentHub package for the molecular signatures database") (description @@ -2326,13 +3092,13 @@ along with the gene set in the @code{GeneSet} class object.") (define-public r-pasilla (package (name "r-pasilla") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pasilla" version 'experiment)) (sha256 - (base32 "0r5i64125qq5z4c8zliazsi68035d1bsz6ingzqdh37m8prdw1cr")))) + (base32 "1pa8s19q1n22nwjwdsdj9sla1x766wr87llxk5jywgfgl49317i7")))) (build-system r-build-system) (propagated-inputs (list r-dexseq)) (native-inputs (list r-knitr)) @@ -2344,16 +3110,65 @@ article 'Conservation of an RNA regulatory map between Drosophila and mammals' by Brooks et al., Genome Research 2011.") (license license:lgpl2.1+))) +(define-public r-pasillabamsubset + (package + (name "r-pasillabamsubset") + (version "0.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pasillaBamSubset" version + 'experiment)) + (sha256 + (base32 "1i1z5vh0clvwrh2dlq0vw61k6nqvm9x7gzqxhm9wx4fxsgry6ncc")))) + (properties `((upstream-name . "pasillaBamSubset"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/pasillaBamSubset") + (synopsis "Subset of BAM files from \"Pasilla\" experiment") + (description + "This package provides a subset of BAM files untreated1.bam (single-end +reads) and untreated3.bam (paired-end reads) from \"Pasilla\" +experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See +the vignette in the pasilla data package for how BAM files untreated1.bam and +untreated3.bam were obtained from the RNA-Seq read sequence data that is +provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to +GSM461181. It also contains the DNA sequence for fly chromosome 4 to which +the reads can be mapped.") + (license license:lgpl2.0+))) + +(define-public r-prolocdata + (package + (name "r-prolocdata") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pRolocdata" version + 'experiment)) + (sha256 + (base32 "0dh5zgwr248gnlygja7ly66dyhh4b4xf72n9ycp0xa02xdl0mwi3")))) + (properties `((upstream-name . "pRolocdata"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-msnbase)) + (native-inputs (list r-testthat)) + (home-page "https://github.com/lgatto/pRolocdata") + (synopsis "Data accompanying the pRoloc package") + (description + "This package provides mass-spectrometry based spatial proteomics data +sets and protein complex separation data. It also contains the time course +expression experiment from Mulvey et al. (2015).") + (license license:gpl2))) + (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) (sha256 - (base32 "18p8hk2dq26pp4fvcf1m8wsvj1mn66i8nr900knl2n9vs09j70wy")))) + (base32 "1mcckdpz4i6azm2dmjrkbn6py4c7bhq1dqzpb3h9am49s1jhzgiw")))) (properties `((upstream-name . "HSMMSingleCell"))) (build-system r-build-system) @@ -2376,13 +3191,13 @@ resulting in a complete gene expression profile for each cell.") (define-public r-all (package (name "r-all") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALL" version 'experiment)) (sha256 - (base32 "1yl8b8q8i19kx4viwinhyq9xn9d4axlfgjvm7cpf7pys4krhnrha")))) + (base32 "0bj7hd0k7rlyh1y68w09s5wpwi68fiw7hsdh0lwmald7x1asbjax")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs @@ -2400,13 +3215,13 @@ the form of an @code{exprSet} object.") (define-public r-affydata (package (name "r-affydata") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affydata" version 'experiment)) (sha256 - (base32 "0srmrb2pf5dhjfm1l1jd06jgnah16qxillxi5zjr8vq7pgvw8x4b")))) + (base32 "1yk3kgyl58wg48004h8249iwbr4g05rkk78rfcdcw4c5r4asfjng")))) (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs @@ -2422,13 +3237,13 @@ package @code{affy}.") (define-public r-gagedata (package (name "r-gagedata") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gageData" version 'experiment)) (sha256 - (base32 "1kbs0fz1jnx3grd9mpclbahwbp3749ipwfs8ggl9299bhjrgh9i6")))) + (base32 "0nbmm17ysyn7sar29sagdhbp2b8zi20ka8l56y9kznaxha7jfk7p")))) (properties `((upstream-name . "gageData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/gageData") @@ -2448,13 +3263,13 @@ yeast are also included.") (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 - (base32 "1xdygjwqgy6kjjxzvsy25bckc0f8j5m42wrj1vrnwy5fp0q7y287")))) + (base32 "006c189pyp3lxmbnygvasayvmv0gzwyrbmn3qgrggmqqhmj5v83q")))) (properties `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) @@ -2465,7 +3280,7 @@ yeast are also included.") r-multiassayexperiment r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description @@ -2481,14 +3296,14 @@ across the entire multi-'omics experiment.") (define-public r-parathyroidse (package (name "r-parathyroidse") - (version "1.42.0") + (version "1.43.0") (source (origin (method url-fetch) (uri (bioconductor-uri "parathyroidSE" version 'experiment)) (sha256 (base32 - "183cyn1i0i2p8npajwmbwzr2ncrrzwgpvh8adhjxzrdqkn3qdnr5")))) + "1kd947b58qvshrzwcxb6gvad5a4xhby68jmwlkfba8h3gpx7vnla")))) (properties `((upstream-name . "parathyroidSE"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -2502,19 +3317,96 @@ cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and contro ;; The author(s) mentions only LGPL without any specific version. (license license:lgpl2.1+))) +(define-public r-rnaseqdata-hnrnpc-bam-chr14 + (package + (name "r-rnaseqdata-hnrnpc-bam-chr14") + (version "0.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RNAseqData.HNRNPC.bam.chr14" version + 'experiment)) + (sha256 + (base32 "1yhr798bbv3mc8wnalz4wag1np6kyq6akb0mbpvj47130ifi0wbx")))) + (properties `((upstream-name . "RNAseqData.HNRNPC.bam.chr14"))) + (build-system r-build-system) + (home-page "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/") + (synopsis + "Aligned reads from RNAseq experiment") + (description + "The package contains 8 BAM files, 1 per sequencing run. Each BAM file +was obtained by aligning the reads (paired-end) to the full hg19 genome with +@code{TopHat2}, and then subsetting to keep only alignments on chr14. See +accession number E-MTAB-1147 in the @code{ArrayExpress} database for details +about the experiment, including links to the published study (by Zarnack et +al., 2012) and to the FASTQ files.") + (license license:lgpl2.0+))) + +(define-public r-rnbeads-hg19 + (package + (name "r-rnbeads-hg19") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RnBeads.hg19" version + 'experiment)) + (sha256 + (base32 "0hvsf3nvyl72rqrwvx54vpca1c445vfchz9h74kd90fgh8crydcm")))) + (properties `((upstream-name . "RnBeads.hg19"))) + (build-system r-build-system) + (propagated-inputs (list r-genomicranges)) + (home-page "https://bioconductor.org/packages/RnBeads.hg19") + (synopsis "RnBeads annotation package for hg19 assembly") + (description + "This package is an automatically generated @code{RnBeads} annotation +package for the assembly hg19.") + (license license:gpl3))) + +(define-public r-rtcga-rnaseq + (package + (name "r-rtcga-rnaseq") + (version "20151101.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RTCGA.rnaseq" version + 'experiment)) + (sha256 + (base32 "0yn89m988gvq4y5nv56581dlh6ydyhd6dkcx1clwalb453v390dz")))) + (properties `((upstream-name . "RTCGA.rnaseq"))) + (build-system r-build-system) + (propagated-inputs (list r-rtcga)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/RTCGA.rnaseq") + (synopsis "Rna-seq datasets from The Cancer Genome Atlas Project") + (description + "This package provides rna-seq datasets from The Cancer Genome Atlas +Project for all cohorts types from @url{http://gdac.broadinstitute.org/}. The +Rna-seq data format is explained here +@url{https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2}. The data source +is Illumina hiseq Level 3 RSEM normalized expression data from 2015-11-01 +snapshot.") + (license license:gpl2))) + (define-public r-sesamedata (package (name "r-sesamedata") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sesameData" version 'experiment)) (sha256 (base32 - "05k67isysszzfkkbi811dkab0cmxnwz81p2ldcqz3gsq5qin3p1g")))) - (properties `((upstream-name . "sesameData"))) + "1dgf9qi27rc98mwlyax0v86h7fmwbnp0xna1c0ppsj0fpwbmj50y")))) + (properties + `((upstream-name . "sesameData") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-sesame")))) (build-system r-build-system) + ;; Tests need r-sesame. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationhub r-experimenthub r-genomeinfodb @@ -2523,7 +3415,7 @@ cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and contro r-readr r-s4vectors r-stringr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/sesameData") (synopsis "Supporting Data for SeSAMe Package") (description @@ -2536,16 +3428,42 @@ currently supports human array (HM27, HM450, EPIC), mouse array (MM285) and the @code{HorvathMethylChip40} (Mammal40) array.") (license license:artistic2.0))) +(define-public r-systempiperdata + (package + (name "r-systempiperdata") + (version "2.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "systemPipeRdata" version + 'experiment)) + (sha256 + (base32 "0276cyzcd9pzma9s4f300snlkyq2xlnavbwm8rwvn22dpgzapskd")))) + (properties `((upstream-name . "systemPipeRdata"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics r-biostrings r-jsonlite r-remotes)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tgirke/systemPipeRdata") + (synopsis "Workflow templates and sample data") + (description + "@code{systemPipeRdata} complements the @code{systemPipeR} workflow +management system (WMS) by offering a collection of pre-designed data analysis +workflow templates. These templates are easily accessible and can be readily +loaded onto a user's system with a single command. Once loaded, the WMS can +immediately utilize these templates for efficient end-to-end analysis, serving +a wide range of data analysis needs.") + (license license:artistic2.0))) + (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment)) (sha256 - (base32 "1r36f7nvvjjgkgmhha81n2iyr9k4nzy0qkkblm483rgzxav4gqa6")))) + (base32 "16ki2mwippf7mk6xrr90m243njvdkdi74yq6lfbklnxsscwcw556")))) (properties `((upstream-name . "TCGAbiolinksGUI.data"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2558,14 +3476,14 @@ TCGAbiolinksGUI package.") (define-public r-tximportdata (package (name "r-tximportdata") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximportData" version 'experiment)) (sha256 (base32 - "15wy0dhs9sbz27ii64b4i0zxlsm6v75m2f32gisdy9f6gnbgwkjg")))) + "1x4c4pd4yyfd8z5gyv7kqiip25bi9mdzl5qix1rb27ljvnyz9405")))) (properties `((upstream-name . "tximportData"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2578,6 +3496,28 @@ quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon} and @code{Sailfish}. Alevin example output is also included.") (license license:gpl2+))) +(define-public r-zebrafishrnaseq + (package + (name "r-zebrafishrnaseq") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zebrafishRNASeq" version + 'experiment)) + (sha256 + (base32 "0h9bgqbyrakpmp15fvwpygmf0yrf8wqyfg3fnr30k46xvn265axh")))) + (properties `((upstream-name . "zebrafishRNASeq"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/zebrafishRNASeq") + (synopsis + "Zebrafish RNA-Seq experimental data from Ferreira et al. (2014)") + (description + "This package provides gene-level read counts from RNA-Seq for +gallein-treated and control zebrafish.") + (license (list license:gpl2+ license:gpl3+)))) + ;;; Packages @@ -2585,13 +3525,13 @@ and @code{Sailfish}. Alevin example output is also included.") (define-public r-abarray (package (name "r-abarray") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "1kfqq4df55pxl7gnwf24aaryxijym4gzqfjyif28arlbjci9hlv6")))) + "0iay7aai5ijg0ai42mz4sks6qvndy69hdwavy5qvbhgfsgbdpmxv")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) @@ -2611,13 +3551,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "0zqb2w055x4whgl3mljarsnps6lkz90fwlx2lnirbnrgmlnalwjz")))) + "02yypkrvd2gbclcddjvw5zdl4crh286ifddxj5cix1d4hhas1gc4")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) @@ -2640,14 +3580,16 @@ ranking by fold-change and visualization.") (define-public r-adacgh2 (package (name "r-adacgh2") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADaCGH2" version)) (sha256 - (base32 "1j9dn0xw8mdfvi2ccm1d5j9q740wb89wqi6715n6jy3dljlc8irz")))) - (properties `((upstream-name . "ADaCGH2"))) + (base32 "1pzzbqh5wflhn9zqpdggx80y6zhdzg6i4xwgzjrh89bq90ibck04")))) + (properties + `((upstream-name . "ADaCGH2") + (updater-extra-inputs . ("python-wrapper")))) (build-system r-build-system) (arguments (list @@ -2681,13 +3623,13 @@ storing data.") (define-public r-adam (package (name "r-adam") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "0z0rmpwfhd8p6c4zscviwsningsm740r3pb95cl8brasfdg1kl3v")))) + "044r6ykd3kv1zswmnw82q961mxywcmxxyj9x55z6qbykww5868lz")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -2699,7 +3641,7 @@ storing data.") r-rcpp r-stringr r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ADAM") (synopsis "Gene activity and diversity analysis module") (description @@ -2716,13 +3658,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "08kxkb6hgbw7l9dv1wn3jfdkc0sizqdgmjkrzpq73q7rf0p4248g")))) + "1gpc5gzrwlji7a0vlr1jidn1c2nkzdv8qb82jhrg5yfglaxf1ddd")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs @@ -2746,7 +3688,7 @@ functionally associated genes} (GFAG).") r-stringr r-testthat r-varhandle)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ADAMgui/") (synopsis "GUI for gene activity and diversity analysis") (description @@ -2764,13 +3706,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0kihg0mwm2ysgnx3jg6xln7ibvgmky0x2hjbcmdqlg65znczh4b6")))) + "1738j07hk2kj7w29vba1xhxnjj5w2zxcf59d3r4mwrxbhc771sqy")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs @@ -2786,7 +3728,7 @@ the @code{GFAGpathUi} function.") r-saver r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ADImpute") (synopsis "Adaptive computational prediction for dropout imputations") (description @@ -2813,13 +3755,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "13rrkb0vxkknvqhb8pgx8d13sxzy3w0wbkhhj5lrlc1kb1yqcfbh")))) + "0x1n2k5pgn5gkfsr15h2vj7mzywxq0b02h6ivwahq2albhmb7ci4")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs @@ -2841,13 +3783,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "1241vpqkv4p3yarr6fsz1a7awvc4ff7q75ia3ra7vgkvg7gx9p93")))) + "1a76l58hl78f0cn602mxxisq7rbgm3ywb45nd20d5h01wmgv3bci")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs @@ -2869,13 +3811,13 @@ expression values are known.") (define-public r-affyilm (package (name "r-affyilm") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyILM" version)) (sha256 - (base32 "185kdrnvcp2jw0k71q0v4yk7583gwgi31h0n281x25hirixf6rm3")))) + (base32 "0x56j63yzssq3brnacz23v02hxlmmki6s89mw09wwhawyia6pv2x")))) (properties `((upstream-name . "affyILM"))) (build-system r-build-system) (propagated-inputs @@ -2896,13 +3838,13 @@ concentrations on behal of the Langmuir model.") (define-public r-affylmgui (package (name "r-affylmgui") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affylmGUI" version)) (sha256 - (base32 "1qilkr3dcl6driah24kgz7lrzamq08qp2z03inm2m4r5yx8811wc")))) + (base32 "11ihq29ydmx264vlgvf923rf3xdspckbgqcjwgwkwvdfa5i6scsp")))) (properties `((upstream-name . "affylmGUI"))) (build-system r-build-system) (propagated-inputs @@ -2928,15 +3870,19 @@ limma packages.") (define-public r-affyplm (package (name "r-affyplm") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyPLM" version)) (sha256 - (base32 "1khknl7k45amyw58mcgw7kl511llyddw31qzwqc2l5c4j3bwnpz5")))) - (properties `((upstream-name . "affyPLM"))) + (base32 "182zym9g8rzyrmj78yzpdh44av616x6228xzxwa45wz2spg9bj47")))) + (properties + `((upstream-name . "affyPLM") + (updater-extra-native-inputs . ("r-hgu95av2cdf")))) (build-system r-build-system) + ;; Tests fail with: return code from pthread_create() is 22 + (arguments (list #:tests? #false)) (inputs (list zlib)) (propagated-inputs (list r-affy @@ -2945,6 +3891,7 @@ limma packages.") r-gcrma r-preprocesscore r-zlibbioc)) + (native-inputs (list r-affydata r-hgu95av2cdf)) (home-page "https://github.com/bmbolstad/affyPLM") (synopsis "Methods for fitting probe-level models") (description @@ -2959,13 +3906,13 @@ also provided.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "19lcs76jsdy5dz57rkdb8qqankpasrw2r5z4cy98q94az6582ix4")))) + "1k7d2w377w9ab7f9j71mc92lx3w851mxbm7lrrbzv63zbv7cynbk")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) @@ -2984,13 +3931,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "088r2ahqjv61wnzp7by4c5v9aivahmyfkzr7prnkk3ff8zh6pznl")))) + "02kldgslgyx5xr5zn45vndai37j66wp4xdjpvasdv46b7rm7drx2")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) @@ -3011,13 +3958,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "0qag99chj7n7l0wbb8ar0f58xs6883rgddkgj7jnrrlj3acrm12v")))) + "00v0chcvisd735f9pyinwn3lg9dq0wdq9jpsm4kp2m45pf22n7p1")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs @@ -3027,7 +3974,7 @@ experiment.") r-singlecellexperiment r-summarizedexperiment r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jasonratcliff/aggregateBioVar") (synopsis "Differential gene expression analysis for multi-subject scRNA-seq") (description @@ -3045,13 +3992,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.36.0") + (version "3.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "1mfi4xvx6ywkr7b7ma9ip6q2nsjvkri8qx48qyr98yyik7gg28d5")))) + "1gzfzbgxb07zmr66h38zy1c1hpb89qnsfg1wsr5p8qwlf76ynzz7")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") @@ -3067,15 +4014,17 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0800jbfm488i6ccz48k49gpxr9sf9104cxcghgy9c4lzm5d3wfbm")))) + "0946x9a2y7yrbgbcn7fmwhkm0caraahl9wcz09aj02gnm5zvlxxs")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) + ;; Tests connect to the internet via r-experimenthub. + (arguments (list #:tests? #false)) (propagated-inputs (list r-adductdata r-ade4 @@ -3098,7 +4047,7 @@ but which also provides utilities which may be useful for other platforms.") r-rvest r-smoother r-zoo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/adductomicsR") (synopsis "Processing of adductomic mass spectral datasets") (description @@ -3112,13 +4061,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "1bm8rxfdgd0fx48fi70by08qr855jv6r4xcr7al2v9akv6vphws2")))) + "1w1x1pzas8vq4x93700j4slkpq3xmwrm3w9zk3nf2366fxrjp65i")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs @@ -3142,16 +4091,17 @@ objects are used so that other packages could be used as well.") (define-public r-aims (package (name "r-aims") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AIMS" version)) (sha256 (base32 - "0ljdv1gww01yi0h9j9br8kp67k5wizr1dy0091kngjcbn0dxzmla")))) + "04xch3ld6f9bwsp3v8m1klxppr52flaj0svk2fjak5m9dar5lg0b")))) (properties `((upstream-name . "AIMS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071)) + (native-inputs (list r-breastcancervdx r-hgu133a-db r-runit)) (home-page "https://git.bioconductor.org/packages/AIMS") (synopsis "Absolute assignment of breast cancer intrinsic molecular subtype") @@ -3166,13 +4116,13 @@ well as on dataset of gene expression data.") (define-public r-airpart (package (name "r-airpart") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 - "05l5rgjfjln3kip72wj4ll4cgak9yz60xg6dgxxj690pxs1pw7bg")))) + "0aggyvbx4vjg3sh4s7jsl2l612vqvgcb2wlymkdjzaj8hykaprvs")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs @@ -3196,7 +4146,7 @@ well as on dataset of gene expression data.") r-singlecellexperiment r-smurf r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/airpart") (synopsis "Differential cell-type-specific allelic imbalance") (description @@ -3213,13 +4163,13 @@ datasets.") (define-public r-alabaster-base (package (name "r-alabaster-base") - (version "1.4.2") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "alabaster.base" version)) (sha256 - (base32 "1yf4j6dwva1d16fb8ss5hrpmj71azwjk9aqpad9wpnfapaldjzhb")))) + (base32 "02bgq5z7p2di62d8167qd02drhrwyjk3c9iq38g7lbk89vbi1f1h")))) (properties `((upstream-name . "alabaster.base"))) (build-system r-build-system) (inputs (list zlib)) @@ -3230,7 +4180,7 @@ datasets.") r-rhdf5 r-rhdf5lib r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/alabaster.base") (synopsis "Save Bioconductor objects to file") (description @@ -3244,13 +4194,13 @@ applications can enrich this metadata with context-specific properties.") (define-public r-alabaster-matrix (package (name "r-alabaster-matrix") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alabaster.matrix" version)) (sha256 - (base32 "1b32qs2baq9s492a332vh1hpyxq62z16xj2w17m8wh8a4mcabry8")))) + (base32 "1pa8ihsiipcmhlm4fczzmlbskai4qlwp7ld65qcznp1bawbxvfhc")))) (properties `((upstream-name . "alabaster.matrix"))) (build-system r-build-system) (propagated-inputs (list r-alabaster-base @@ -3263,7 +4213,7 @@ applications can enrich this metadata with context-specific properties.") r-s4arrays r-s4vectors r-sparsearray)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/alabaster.matrix") (synopsis "Load and save artifacts from file") (description @@ -3277,13 +4227,13 @@ can enrich this metadata with context-specific properties.") (define-public r-alabaster-ranges (package (name "r-alabaster-ranges") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alabaster.ranges" version)) (sha256 - (base32 "16r5wdlw2g9qnbvzpx5c5c04xa5dkwrmqlyc81iixkx6j98gsz2w")))) + (base32 "06xky6gdwhvz09v6yafwr65lq3bj4s8qz5iqpp120m9nncfzf1f4")))) (properties `((upstream-name . "alabaster.ranges"))) (build-system r-build-system) (propagated-inputs (list r-alabaster-base @@ -3293,7 +4243,7 @@ can enrich this metadata with context-specific properties.") r-iranges r-rhdf5 r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/alabaster.ranges") (synopsis "Load and save Ranges-related artifacts from file") (description @@ -3308,18 +4258,18 @@ context-specific properties.") (define-public r-alabaster-sce (package (name "r-alabaster-sce") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alabaster.sce" version)) (sha256 - (base32 "1i9nmivsfrd7fbb8njmwihfx4xpj4p3h5bnlj9fvk5308bbj3qcg")))) + (base32 "0ddi6y2c8csxrzqv5h0lmxvhvhiz285f0hd01q8mpn9rs4n5cljs")))) (properties `((upstream-name . "alabaster.sce"))) (build-system r-build-system) (propagated-inputs (list r-alabaster-base r-alabaster-se r-jsonlite r-singlecellexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/alabaster.sce") (synopsis "Load and save SingleCellExperiment from file") (description @@ -3333,13 +4283,13 @@ can enrich this metadata with context-specific properties.") (define-public r-alabaster-schemas (package (name "r-alabaster-schemas") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alabaster.schemas" version)) (sha256 - (base32 "1cizlslxw0nhrfjsz3x90waa9w4n2v72a0cycbzvxqbbvkh3cp1l")))) + (base32 "0sqkm3f1vha1iw8az0giz7yj78b75dh4g9qkly0yd3bpmb9g3zd9")))) (properties `((upstream-name . "alabaster.schemas"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3354,13 +4304,13 @@ handled by @code{alabaster.base}.") (define-public r-alabaster-se (package (name "r-alabaster-se") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alabaster.se" version)) (sha256 - (base32 "134r4pwaa4nsmdgqxs16w3adn482zl70lgyd4s96pmx7hqm9i1vx")))) + (base32 "01963yn5iyc0ksxr1nlwkddfll9259x2w3y1b82db36kjj3bac2y")))) (properties `((upstream-name . "alabaster.se"))) (build-system r-build-system) (propagated-inputs (list r-alabaster-base @@ -3372,7 +4322,7 @@ handled by @code{alabaster.base}.") r-jsonlite r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/alabaster.se") (synopsis "Load and save SummarizedExperiments from file") (description @@ -3386,13 +4336,13 @@ can enrich this metadata with context-specific properties.") (define-public r-amountain (package (name "r-amountain") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "1y2k1vg31siic6j98700m54sswbj6wr4dvbw2mz3hlm0nmsmpxc1")))) + "0w1m0y9q7vksxnhxa8gz3fl47niss7zcbvvrjsdrf82yx6x8vp6j")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) @@ -3410,13 +4360,13 @@ in multi-layer WGCN using a continuous optimization approach.") (define-public r-amplican (package (name "r-amplican") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "amplican" version)) (sha256 (base32 - "1nbyivd5020kqkmk5ngpaixhdxgmqpifaxnfgq6yc2njqizgbhxy")))) + "1xv392kxhzal2b8dp0kdjnny75311qm6vvbajx9hlb3k6v34dpqc")))) (properties `((upstream-name . "amplican"))) (build-system r-build-system) (propagated-inputs @@ -3443,7 +4393,7 @@ in multi-layer WGCN using a continuous optimization approach.") r-shortread r-stringr r-waffle)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/valenlab/amplican") (synopsis "Automated analysis of CRISPR experiments") (description @@ -3458,13 +4408,13 @@ problems.") (define-public r-amaretto (package (name "r-amaretto") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "0n3w00x1qajkg43ip3l63k2qs0d1x2zv8wv4xj0iqwl6r6cqgxnf")))) + "0lk7rd4ipwgx2mzwwy9kc4ngd9849p804499xdwy2j4ygq01zrkq")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs @@ -3492,7 +4442,7 @@ problems.") r-reshape2 r-rmarkdown r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/AMARETTO") (synopsis "Regulatory network inference and driver gene evaluation") (description @@ -3510,13 +4460,13 @@ canonical cancer pathways.") (define-public r-anaquin (package (name "r-anaquin") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "0hfvwzkfy6bm2ffghax5b228k2l6wf8zq82q13h6bxfps4wz0jgb")))) + "0krfyb0bcc4vpna7ygyd9rqsdpnqmizlmf8sgpcyfk722dbavvdn")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs @@ -3527,7 +4477,7 @@ canonical cancer pathways.") r-plyr r-qvalue r-rocr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://www.sequinstandards.com/") (synopsis "Statistical analysis of sequins") (description @@ -3540,13 +4490,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "14jdfcv3hghl1z2f7zj2mdqdyblz5sn4l1iwh8bhvih86cpigb58")))) + "0cbz7yxrci57divf85d9ffkzi1rh7xy2ara9x1wng75vc0qcnj9c")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -3562,15 +4512,10 @@ analysis, modelling, and visualization of spike-in controls.") r-lmertest r-mass r-matrix - r-mia r-multcomp r-nloptr - r-rdpack - r-s4vectors - r-singlecellexperiment - r-summarizedexperiment - r-treesummarizedexperiment)) - (native-inputs (list r-knitr)) + r-rdpack)) + (native-inputs (list r-knitr r-microbiome r-testthat)) (home-page "https://github.com/FrederickHuangLin/ANCOMBC") (synopsis "Analysis of compositions of microbiomes with bias correction") (description @@ -3589,13 +4534,13 @@ these biases and construct statistically consistent estimators.") (define-public r-animalcules (package (name "r-animalcules") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "animalcules" version)) (sha256 (base32 - "1g073n8nmckd388hy9gfiddil53wv692k69ywjc85jyp5jy2n265")))) + "02dbfx159b9ivlzgyhd1ikhw2ciq6q7f3b3sdq4hsp49yp6ps7nl")))) (properties `((upstream-name . "animalcules"))) (build-system r-build-system) (propagated-inputs @@ -3630,7 +4575,7 @@ these biases and construct statistically consistent estimators.") r-umap r-vegan r-xml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/compbiomed/animalcules") (synopsis "Interactive microbiome analysis toolkit") (description @@ -3648,19 +4593,25 @@ to understand their data better and discover new insights.") (define-public r-annotationhubdata (package (name "r-annotationhubdata") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHubData" version)) (sha256 - (base32 "0wcbghjvgr8sx1qg9kyjxb7znkxhihy7jvzycrv4pyq746154xbi")))) + (base32 "0b279vpqyq4a88w543yj9hwlifl0c1qxjvz1msrxxxibz21fk3r8")))) (properties `((upstream-name . "AnnotationHubData"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests require internet access. + (for-each delete-file + '("inst/unitTests/test_recipe.R" + "inst/unitTests/test_webAccessFunctions.R")))) (add-before 'install 'set-home (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs @@ -3688,7 +4639,7 @@ to understand their data better and discover new insights.") r-rtracklayer r-s4vectors r-xml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/AnnotationHubData") (synopsis "Transform public data resources into Bioconductor data structures") (description @@ -3699,17 +4650,18 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "0i4skg2bpj0rbb3fbaprfs4d4nxg9aj8d6pni4a3k0wip3dw1cf9")))) + "101d8xc8ifyxgnwp0a60r55pqfpmp8cfbbnmy0z8r95r2nylzxsg")))) (properties `((upstream-name . "AnVIL"))) (build-system r-build-system) (propagated-inputs - (list r-biocbaseutils + (list r-anvilbase + r-biocbaseutils r-biocmanager r-dplyr r-dt @@ -3725,7 +4677,7 @@ for use in Bioconductor’s AnnotationHub.") r-tidyr r-tidyselect r-yaml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/AnVIL") (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects") (description @@ -3739,16 +4691,39 @@ Dockstore, and Gen3 RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.") (license license:artistic2.0))) +(define-public r-anvilbase + (package + (name "r-anvilbase") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnVILBase" version)) + (sha256 + (base32 "0cjik5yvbbpryyawkqb6y38h92in0jkkm46a4kisbsif42hwa2i5")))) + (properties `((upstream-name . "AnVILBase"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr r-httr r-httr2 r-jsonlite r-tibble)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/Bioconductor/AnVILBase") + (synopsis "Generic functions for interacting with the AnVIL system") + (description + "This package provides generic functions for interacting with the +@code{AnVIL} system. Packages that use either GCP or Azure in @code{AnVIL} +are built on top of @code{AnVILBase}. Extension packages will provide methods +for interacting with other cloud providers.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALDEx2" version)) (sha256 (base32 - "1bqpk93bbyajw2dm54d68f3dkc0jgcny109asfm6kcz7dg7szi3y")))) + "1c22h27w852b5mbniw6266r8pxf28ii5czi8iki6ik9k3l4n6xzd")))) (properties `((upstream-name . "ALDEx2"))) (build-system r-build-system) (propagated-inputs @@ -3763,7 +4738,7 @@ to transform JSON responses to formats more amenable to manipulation in R.") r-s4vectors r-summarizedexperiment r-zcompositions)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ggloor/ALDEx_bioc") (synopsis "Analysis of differential abundance taking sample variation into account") (description @@ -3786,13 +4761,13 @@ paired or unpaired study designs.") (define-public r-alevinqc (package (name "r-alevinqc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alevinQC" version)) (sha256 (base32 - "1pq42lvgggysg28ngxipqb1l7jfj498nxpg40h02siz6nb6inbdw")))) + "01ywmi5k5y9x5ds743qhzjn975gc5h8k0csxs78pnrjng5ij2gh2")))) (properties `((upstream-name . "alevinQC"))) (build-system r-build-system) (propagated-inputs @@ -3808,7 +4783,7 @@ paired or unpaired study designs.") r-shiny r-shinydashboard r-tximport)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/csoneson/alevinQC") (synopsis "Quality control reports for @code{Alevin} output") (description @@ -3820,13 +4795,13 @@ generated as HTML or PDF files, or as Shiny applications.") (define-public r-alphabeta (package (name "r-alphabeta") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlphaBeta" version)) (sha256 (base32 - "192jyfw2676x8pgcp9h4d78283p7n6gnsdw7wzphfjn12v266fb5")))) + "0zyf38xa5dbk8n71l1bgk1d49ic0f009nggajggyhgsrgf5j14gr")))) (properties `((upstream-name . "AlphaBeta"))) (build-system r-build-system) (propagated-inputs @@ -3882,7 +4857,7 @@ plants. The method has been specifically designed to: r-speedglm r-stringr r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/alpine") (synopsis "Modeling and correcting fragment sequence bias") (description @@ -3900,13 +4875,13 @@ data.") (define-public r-alpsnmr (package (name "r-alpsnmr") - (version "4.6.0") + (version "4.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlpsNMR" version)) (sha256 (base32 - "1c8ynw9424ygc4wj4drbm9gdkdqwgb5z7p72zk3x5zh3zqai0d1d")))) + "0aqf87i96fgbjkwkpa86k6kika0xz5f1jw6zs1sjq56q63xnd4bx")))) (properties `((upstream-name . "AlpsNMR"))) (build-system r-build-system) (propagated-inputs @@ -3915,7 +4890,6 @@ data.") r-cli r-dplyr r-fs - r-future r-generics r-ggplot2 r-glue @@ -3937,7 +4911,7 @@ data.") r-tidyr r-tidyselect r-vctrs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://sipss.github.io/AlpsNMR/") (synopsis "Automated spectral processing system for NMR") (description @@ -3954,13 +4928,13 @@ data. Efficient plotting with 1-D data is also available. Basic reading of (define-public r-altcdfenvs (package (name "r-altcdfenvs") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "altcdfenvs" version)) (sha256 (base32 - "08k3j3dc93vg5c9ccw7mc4fri9xbdj7rdjyj0h6ig0s5866fqvlb")))) + "1fj22d7c8gid26x7383ihq82yfcnpyljl0qk4yh48p8qhgh3wysa")))) (properties `((upstream-name . "altcdfenvs"))) (build-system r-build-system) (propagated-inputs @@ -3985,16 +4959,16 @@ create an alternative mapping from sequences.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "0dgmg0slyrh025wgz299dzzmpirlmdhmabxspci1qfarakw5yicf")))) + "0zqbpip172w02d9iw3n10b0c3pcnk63fp28m886333wcsm7j84b0")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (propagated-inputs (list r-aneufinderdata r-bamsignals @@ -4026,22 +5000,24 @@ sequencing data.") (define-public r-anf (package (name "r-anf") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "00s2rlkh5snqmvlz5a21ilmm0ngh4g362y7iayr6f78nh8gwp617")))) + "1v1lzd0lbg21z1gyca1p45p50akznjlq0b3999sny7hfh20954fr")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) + ;; Tests attempt to download data files. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biobase r-igraph r-mass r-rcolorbrewer r-survival)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ANF") (synopsis "Affinity network fusion for complex patient clustering") (description @@ -4054,15 +5030,22 @@ network fusion.") (define-public r-annmap (package (name "r-annmap") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "1xijcm0c19wj2yknrlsz2ifm097z32rc58k608482686srj0bg2i")))) + "0rq8v5dfmmr43nyri3yr2q4wcq7p9c0ia3nfj4ry5xpkiyqj4n1x")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Needed for tests. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-biobase r-biocgenerics @@ -4074,6 +5057,7 @@ network fusion.") r-lattice r-rmysql r-rsamtools)) + (native-inputs (list r-runit)) (home-page "https://github.com/cruk-mi/annmap") (synopsis "Genome annotation and visualisation for Affymetrix arrays and NGS analysis") @@ -4088,13 +5072,13 @@ Functions to plot gene architecture and BAM file data are also provided.") (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "0p2fhxzgn877mic2yv1sgcidgm74z8hxa3hdaawgvhhvi2j6v8wa")))) + "0xg1kjb0g7cxkj6qv2979n9yfyfwgfllzi2zp9jaml6cw30ma0ya")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs @@ -4114,13 +5098,13 @@ tumor samples from healthy controls.") (define-public r-arrayexpress (package (name "r-arrayexpress") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ArrayExpress" version)) (sha256 (base32 - "1ad6h0pi04r9m3nwxrn7sha837m95kwii8z6s7j4zbka9ijy2pr4")))) + "1ngmgf05zxdhgg15c8qplc04j5azr4kjw0x4s0hcvrjay6kimvlw")))) (properties `((upstream-name . "ArrayExpress"))) (build-system r-build-system) (propagated-inputs @@ -4141,13 +5125,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (define-public r-arrayqualitymetrics (package (name "r-arrayqualitymetrics") - (version "3.60.0") + (version "3.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayQualityMetrics" version)) (sha256 (base32 - "04y1vbpxqhqn1vsyqmscikaxn6wshsk4krcqzf2baf9x4azbdjk1")))) + "04xc1kqz26l74hsrk6p5bj6c3i5pc19v7y1rwz46wszk40p1rln5")))) (properties `((upstream-name . "arrayQualityMetrics"))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -4179,13 +5163,13 @@ supported.") (define-public r-arraymvout (package (name "r-arraymvout") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayMvout" version)) (sha256 - (base32 "11v3s972nyahdswqdcab0fj9jb73vd5dnd5kfb09572y4z0hn5xw")))) + (base32 "0hfal4q9l8g0nfmp2835qagym4hx7xnbic0xh8653lxsy7sbimf0")))) (properties `((upstream-name . "arrayMvout"))) (build-system r-build-system) (arguments @@ -4215,13 +5199,13 @@ fixed Type I error rate.") (define-public r-arrayquality (package (name "r-arrayquality") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayQuality" version)) (sha256 - (base32 "0wmczy2wdxki9pam9q6ly5clvqbl018v1ar4zkdm8algjddyc2cp")))) + (base32 "0rsb1gxy34jyacmy6w5av9gisknb1pqi7irjqimgaqzyvq00hzal")))) (properties `((upstream-name . "arrayQuality"))) (build-system r-build-system) (propagated-inputs @@ -4240,16 +5224,16 @@ quality assessment.") (define-public r-asafe (package (name "r-asafe") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASAFE" version)) (sha256 (base32 - "13qf4jvf0m6i46bwqxdhd4zllac370ckwnd9xh6p56r1lrgcl4sa")))) + "0q7rv3aasc8xdl0mamggncgs2cdyqyagq4rnskc0c3qccb7mvakg")))) (properties `((upstream-name . "ASAFE"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ASAFE") (synopsis "Ancestry Specific Allele Frequency Estimation") (description @@ -4263,13 +5247,13 @@ pairs.") (define-public r-aseb (package (name "r-aseb") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1h5rgy2n7rxd72ypzwnfclw8h5hvdnac48fgbfll669z2k97dsmm")))) + "0ks9h4gzsjpjjwifscid9y175kdshqng22rqc129fq4ch17pd0bs")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") @@ -4290,13 +5274,13 @@ RNAs.") (define-public r-asgsca (package (name "r-asgsca") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASGSCA" version)) (sha256 (base32 - "0gvpb1pspm7zlllg77fbi3g6csa3cpp2lbljna2m0xfi0c5zdqvw")))) + "1c004m9n7z7xg15pd212gjxsawir68xvqrhsxgsm5vz7viwmyqqr")))) (properties `((upstream-name . "ASGSCA"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) @@ -4313,13 +5297,13 @@ model as latent variables.") (define-public r-asics (package (name "r-asics") - (version "2.20.1") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASICS" version)) (sha256 (base32 - "0halznbl3bflnn38rh9h5a5f0dsc88n6x6kwdffbpnin9i192q1k")))) + "1ab8j2rmqig1c25z70ys5ip9818idy0md2a755lz0jcy0srk425j")))) (properties `((upstream-name . "ASICS"))) (build-system r-build-system) (propagated-inputs @@ -4335,7 +5319,7 @@ model as latent variables.") r-ropls r-summarizedexperiment r-zoo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ASICS") (synopsis "Automatic statistical identification in complex spectra") (description @@ -4347,13 +5331,13 @@ the spectra of the library with a sparse penalty.") (define-public r-aspli (package (name "r-aspli") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASpli" version)) (sha256 (base32 - "1br4apbc3zn06ilg8fjb8xcxaimz4h7rnx9i60ak4wnpvgzgbyh2")))) + "160cdm2f8mi3smnx5svaw0mhwnvcmqrl8hikhwj69fygh0razfix")))) (properties `((upstream-name . "ASpli"))) (build-system r-build-system) (propagated-inputs @@ -4396,13 +5380,13 @@ that might arise in splicing patterns.") (define-public r-assessorf (package (name "r-assessorf") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AssessORF" version)) (sha256 (base32 - "1gzaafsfqzy2x35i251gvkd1syif80qb08kkvgnf1i6c8d2czmps")))) + "1q0m5a9wqqn1mm8mkqyqs85g33a6pccgxbzlgwimihdbxhddg9qd")))) (properties `((upstream-name . "AssessORF"))) (build-system r-build-system) (propagated-inputs @@ -4425,17 +5409,17 @@ start codons as the forms of evidence.") (define-public r-asset (package (name "r-asset") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASSET" version)) (sha256 (base32 - "1wqsnp7w3ml7azrx72fafcfbmjg4324jaxcijpcrlrrccxl5rwp4")))) + "0lq07mq7ai51c1dkjkmjrafq3caw6wpzrpbfsbqa3dyjn3vp3c04")))) (properties `((upstream-name . "ASSET"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-rmeta)) - (native-inputs (list r-knitr)) + (native-inputs (list r-biocgenerics r-knitr r-runit)) (home-page "https://bioconductor.org/packages/ASSET") (synopsis "Subset-based association analysis of heterogeneous traits and subtypes") @@ -4449,16 +5433,40 @@ searching for the best combination of disease subtypes associated with each variant.") (license license:gpl2))) +(define-public r-assorthead + (package + (name "r-assorthead") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "assorthead" version)) + (sha256 + (base32 "120x9xz373zm8p1m1bky0gn82qw3pm8dff3sp2farjr7p5phi7b6")))) + (properties `((upstream-name . "assorthead"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/LTLA/assorthead") + (synopsis "Assorted header-only C++ libraries") + (description + "This package vendors an assortment of useful header-only C++ libraries. +Bioconductor packages can use these libraries in their own C++ code by +@code{LinkingTo} this package without introducing any additional dependencies. +The use of a central repository avoids duplicate vendoring of libraries across +multiple R packages, and enables better coordination of version updates across +cohorts of interdependent C++ libraries.") + (license license:expat))) + (define-public r-atena (package (name "r-atena") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "1y2v8mi9awgfbcawpcir01qglxn0bdgj6v2dsdqp6if25cizl3sr")))) + "15dvcymd9svp0mw6s0qrfnsc8zlnvxz1lmkzns0rm8ivflf36q1r")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs @@ -4479,7 +5487,7 @@ variant.") r-sparsematrixstats r-squarem r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://github.com/functionalgenomics/atena") (synopsis "Analysis of transposable elements") (description @@ -4496,13 +5504,13 @@ transcripts in an integrated manner.") (define-public r-atsnp (package (name "r-atsnp") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atSNP" version)) (sha256 (base32 - "08pcbys8iy8wzqzzvlnwc3qw7m7cswkqa3x2x2x8m4ni1s4isd6z")))) + "04gawccjzgjbzrvb98djf9g07pb812rkdwwv3hhbr4sp02yr9hr1")))) (properties `((upstream-name . "atSNP"))) (build-system r-build-system) (propagated-inputs @@ -4516,7 +5524,7 @@ transcripts in an integrated manner.") r-rappdirs r-rcpp r-testthat)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/sunyoungshin/atSNP") (synopsis "Affinity test for identifying regulatory single nucleotide polymorphisms") @@ -4529,13 +5537,13 @@ SNP-led changes in motif matches.") (define-public r-attract (package (name "r-attract") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "attract" version)) (sha256 (base32 - "08l634sk6y06y2m78vsd0ld4w3h6qvx4hk6wkqflkl9jjyqpx8jy")))) + "1nlfnrf7brlqlb7dqzmzqyv6xca5axs1044j22m8lrgwjjpc5xry")))) (properties `((upstream-name . "attract"))) (build-system r-build-system) (propagated-inputs @@ -4560,13 +5568,13 @@ transcriptionally-coordinated changes in gene expression.") (define-public r-awfisher (package (name "r-awfisher") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AWFisher" version)) (sha256 (base32 - "0z5qs337zqqri2g3m69m85xg4x5sxnqlkbwz83vhnqfzmy9nqym0")))) + "040x6millcnii58q441zh99zkskl0v1s9g9cx54srhca25qywfnr")))) (properties `((upstream-name . "AWFisher"))) (build-system r-build-system) (propagated-inputs @@ -4584,17 +5592,17 @@ meta-pattern.") (define-public r-awst (package (name "r-awst") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "awst" version)) (sha256 (base32 - "1iaakdjxrz4szl4lnjcszy47q5dsh2d7i3wrr3wwdhw6wjcd62hj")))) + "1l23vnp5xwl61ag4djvsg06dp543il8rv3an6hs1qi1wd1lk3llh")))) (properties `((upstream-name . "awst"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/drisso/awst") (synopsis "Asymmetric within-sample transformation") (description @@ -4611,13 +5619,13 @@ artifacts.") (define-public r-baalchip (package (name "r-baalchip") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaalChIP" version)) (sha256 (base32 - "1xm6czgbfz2rjrz5996d0n7xmlh9pd1mw9i8ac66pmn5fi44pbz2")))) + "0zhxsw1sbk6kmxm9ypw211ybdn29lid5r2cjz7j855822afgg0l4")))) (properties `((upstream-name . "BaalChIP"))) (build-system r-build-system) (inputs (list)) ; extra/get.overlaps.v2_chrXY.perl @@ -4634,7 +5642,7 @@ artifacts.") r-reshape2 r-rsamtools r-scales)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/BaalChIP") (synopsis "Analysis of allele-specific transcription factor binding in cancer genomes") @@ -4651,13 +5659,13 @@ alleles, a known phenotypical feature of cancer samples.") (define-public r-bags (package (name "r-bags") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BAGS" version)) (sha256 - (base32 "1xc7gp5fljqz26lj8sjcilm01g636p4wlzy4pzy5wgqxgfcw3zps")))) + (base32 "0wv55pmn0435wn4as4r1ihf8w82v2a95n59wq94n25lx46gzjih7")))) (properties `((upstream-name . "BAGS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-breastcancervdx)) @@ -4672,16 +5680,17 @@ interest.") (define-public r-basespacer (package (name "r-basespacer") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaseSpaceR" version)) (sha256 (base32 - "02f2l42p08xags155qydz97ipg5vya0prmrlw4kvahgbq5p0xm44")))) + "1fbj41m9rqg1x6lmklk5zkq2hn5vvv2w693i5xv7nw0rprbjq5x3")))) (properties `((upstream-name . "BaseSpaceR"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/BaseSpaceR") (synopsis "R SDK for BaseSpace RESTful API") (description @@ -4719,13 +5728,13 @@ you will have to normalize your data beforehand.") (define-public r-bader (package (name "r-bader") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BADER" version)) (sha256 (base32 - "15lsvfmp4qsrv12bcrz5q8yz8xyg9rckrcflr3k6si03z2vw812p")))) + "1bksx6a0xg7hd3nd32d5pjfwb9iy64asvdp6drwlkyxv9fys976y")))) (properties `((upstream-name . "BADER"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BADER") @@ -4743,13 +5752,13 @@ can be used for further down-stream analyses such as gene set enrichment.") (define-public r-badregionfinder (package (name "r-badregionfinder") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BadRegionFinder" version)) (sha256 (base32 - "1hs1mv8gj4w0wk6sw6r08j237vw3lhjrv9zip5nk6l1g1r0pg597")))) + "1xnzg4vaadh46dyqrrk1srzxkm57bkwm942xrsvlf46vibd4l9iw")))) (properties `((upstream-name . "BadRegionFinder"))) (build-system r-build-system) (propagated-inputs @@ -4770,13 +5779,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "1pn6a74nvcpn0xzfb8167hbc6pdma0ybhh7kjpqdl4hgjp446w5w")))) + "1jh1qvscwd2fkyb0vzj93kh27h3qssif5fh2z365yvp3pz4asy1j")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -4797,7 +5806,7 @@ Various visual and textual types of output are available.") r-summarizedexperiment r-tidyr r-xgboost)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/GoekeLab/bambu") (synopsis "Isoform reconstruction and quantification for long read RNA-Seq data") @@ -4813,13 +5822,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "1iizs0bvs7rbkwv3vs6xk26jy222kql80fp6cki0qs9h9igpzk5h")))) + "01ksk9wqzmg14pn0x0dch1fcrdwxw9qrfc592gkx9cy4sh8kdf3n")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -4834,7 +5843,7 @@ usage.") r-r-utils r-rcpp r-rcpparmadillo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/SimoneTiberi/BANDITS") (synopsis "Bayesian analysis of differential splicing") (description @@ -4851,13 +5860,13 @@ the posterior densities for the average relative abundance of transcripts.") (define-public r-banocc (package (name "r-banocc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "banocc" version)) (sha256 (base32 - "12fysw9m3rrmyfq1j97rdklaln6vgjdmz7hj85vrh10haz9j23s2")))) + "1npmkj4a834k4kkaa6az94mzs17nhqq1i74zg7s81n3xi4ghd66k")))) (properties `((upstream-name . "banocc"))) (build-system r-build-system) (propagated-inputs @@ -4865,7 +5874,7 @@ the posterior densities for the average relative abundance of transcripts.") r-mvtnorm r-rstan r-stringr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/banocc") (synopsis "Bayesian analysis of compositional covariance") (description @@ -4879,13 +5888,13 @@ estimates for each correlation element.") (define-public r-barcodetrackr (package (name "r-barcodetrackr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 - "0x0fpa44lyww2l1rdc35pdlgczz4y1vxjbn0s1frlpaacmqcxrly")))) + "1vmfq5llvg7s8f919jafllip2v710sqsrpfxa8imjg30hr9h9fkl")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs @@ -4908,7 +5917,7 @@ estimates for each correlation element.") r-tidyr r-vegan r-viridis)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/dunbarlabNIH/barcodetrackR") (synopsis "Functions for analyzing cellular barcoding data") (description @@ -4921,14 +5930,14 @@ retrieval analyses, or similar technologies.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.19.1") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "1zhm28313gsbscfhfdbqizvb5v67n4l0dapjmb1xq010ikly95mh")))) + "1ixn9pwzm15z79da90iqniv8c6x8w7k5wdwzpj9dm1ghwd04xqcx")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -4941,16 +5950,18 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.50.0") + (version "0.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0500ya3df53xx1dfdmk50bh30ja28y6qkdwds1c1m4c7q0h2xmqi")))) + "1nbzbrb07v7wx19qhm65py9bl7ij4bpiqw87ixd00b6w6j6nmx8l")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) + ;; Tests require r-iranges, which needs this package. + (arguments (list #:tests? #false)) (home-page "https://bioconductor.org/packages/BiocGenerics") (synopsis "S4 generic functions for Bioconductor") (description @@ -4961,13 +5972,13 @@ packages.") (define-public r-breakpointr (package (name "r-breakpointr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breakpointR" version)) (sha256 (base32 - "0imbsqrslclvfyvc00sv6ngvl5hqlr6ian07v521m63ffpx6ll78")))) + "0x95r30dvkkpsbang8vj0xg4mc48ljc5ci318m55n92lk0lfzpa0")))) (properties `((upstream-name . "breakpointR"))) (build-system r-build-system) (propagated-inputs @@ -4984,7 +5995,7 @@ packages.") r-iranges r-rsamtools r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/daewoooo/BreakPointR") (synopsis "Find breakpoints in Strand-seq data") (description @@ -4995,13 +6006,13 @@ export of Strand-seq data.") (define-public r-cardelino (package (name "r-cardelino") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cardelino" version)) (sha256 (base32 - "16mczwh41gf7ikbzxvggai7a8d64fn2k7q9w1yxf0sn6cwg3l0di")))) + "1zglflqc53izs5rh8cdld0y129mdvwlhmv9pgbgrl4clcnnbiwac")))) (properties `((upstream-name . "cardelino"))) (build-system r-build-system) (propagated-inputs (list r-combinat @@ -5016,7 +6027,7 @@ export of Strand-seq data.") r-snpstats r-variantannotation r-vcfr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/single-cell-genetics/cardelino") (synopsis "Clone identification from single cell data") (description @@ -5030,16 +6041,59 @@ scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.") (license license:gpl3))) +(define-public r-ccfindr + (package + (name "r-ccfindr") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ccfindR" version)) + (sha256 + (base32 "1v8lrgs5rqf0pz5gg7g5hh9y7cj90s8k04bhimhlzr0iah27vhc5")))) + (properties + `((upstream-name . "ccfindR") + (updater-extra-inputs . ("gsl")))) + (build-system r-build-system) + (inputs (list gsl)) + (propagated-inputs (list r-ape + r-gtools + r-irlba + r-matrix + r-rcolorbrewer + r-rcpp + r-rcppeigen + r-rdpack + r-rmpi + r-rtsne + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://dx.doi.org/10.26508/lsa.201900443") + (synopsis "Cancer clone finder") + (description + "This package provides a collection of tools for cancer genomic data +clustering analyses, including those for single cell RNA-seq. Cell clustering +and feature gene selection analysis employ Bayesian (and maximum likelihood) +non-negative matrix factorization (NMF) algorithm. Input data set consists of +RNA count matrix, gene, and cell bar code annotations. Analysis outputs are +factor matrices for multiple ranks and marginal likelihood values for each +rank. The package includes utilities for downstream analyses, including +meta-gene identification, visualization, and construction of rank-based trees +for clusters.") + (license license:gpl2+))) + (define-public r-cellid (package (name "r-cellid") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CelliD" version)) (sha256 (base32 - "0c7hls5qasjd5ahrqxp2mpd402jc12pi0pgy7spcbp1fkqm8qvbl")))) + "0qgkyl57ggkx9577a6lvpxb3vcqhjgi5r1l56xbxniphjcq41cpy")))) (properties `((upstream-name . "CelliD"))) (build-system r-build-system) (propagated-inputs @@ -5064,7 +6118,7 @@ stochastic dropout events as well as systematic allelic imbalance is used.") r-summarizedexperiment r-tictoc r-umap)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/CelliD") (synopsis "Single cell gene signature extraction using multiple correspondence analysis") @@ -5079,13 +6133,13 @@ enrichment in single cell data.") (define-public r-coregx (package (name "r-coregx") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoreGx" version)) (sha256 - (base32 "05fyncpqiq08a169rjwyc117wkyckh714z0is2r0g79920i36jas")))) + (base32 "0lw1fby6jxkz6bcbvlz8yqa8p00k85bay59lsr2qk5qlbsgz894a")))) (properties `((upstream-name . "CoreGx"))) (build-system r-build-system) (propagated-inputs @@ -5105,7 +6159,7 @@ enrichment in single cell data.") r-rlang r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/CoreGx") (synopsis "Classes and functions to serve as the basis for other Gx packages") @@ -5124,13 +6178,13 @@ the curve} or @acronym{SF, survival fraction} are included.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1wgkn2adcxl6js3cvawhvzpxm3nmnnc16wbnzkrnsnd9l12aasih")))) + "0r9g6iwbgf1dfi606cgzi32bjp57f7dfzpjx1fa3y3z6ikffjykb")))) (build-system r-build-system) (propagated-inputs (list r-genomicalignments @@ -5151,13 +6205,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "0hdm2214waz02ybr264xis48kj2anpad80jk640p49v9r17iia9l")))) + "13505rlzwczgqzqs9fcfgij8558iwzhcn29ai4xl96qqz4qwx00k")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -5181,13 +6235,13 @@ used visualizations.") (define-public r-dama (package (name "r-dama") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "daMA" version)) (sha256 (base32 - "1hv43r6rymp09fl7vgr8jf6naixkrgl282ggf6nva0jxf1jnfmb3")))) + "1gxh344z7jjisb5s8w3q1ky87ryn2n55ayadpwxdimqh2acbz9r5")))) (properties `((upstream-name . "daMA"))) (build-system r-build-system) (propagated-inputs (list r-mass)) @@ -5203,13 +6257,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "1ffqa7a3a0f3m58j6al2hd7aa8bamv4z170y4yn1vr1f8jrb7kq5")))) + "03lk5i1sc0jfzw4qkhbkzjl86xqnv9v1398z5ykiajw8cama0lkq")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs @@ -5231,7 +6285,7 @@ factorial microarray data.") r-stringr r-summarizedexperiment r-variantannotation)) - (native-inputs (list r-knitr)) + (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/DAMEfinder") (synopsis "Differential allelicly methylated regions") (description @@ -5244,14 +6298,14 @@ offers nice visualization of methyl-circle plots.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "0hy8cnqyvp2mrhj5wi1shh1cba79c5z8f17mfw764s2d6ivsfzz6")))) + "0mk8flxgifwg8ckf41abiqqjmqi1217rrxqwg2xk26s4dk81m4pp")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -5270,7 +6324,7 @@ offers nice visualization of methyl-circle plots.") r-tibble r-viridislite)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/borishejblum/dearseq") (synopsis "DEA for RNA-seq data through a robust variance component test") (description @@ -5283,13 +6337,13 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-debcam (package (name "r-debcam") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "1lbgwv7009fpwqw6kl94gmm44xypn60r8kcm3fjzgbjbwijriwgq")) + "0wx6dvi5rihxlzm6wn67r5wni3dmk12fih2s0dw9qnwm56zk96a5")) (snippet '(for-each delete-file '("inst/java/CornerDetect.jar" @@ -5340,7 +6394,7 @@ set analyses, and can deal with repeated or longitudinal data.") r-rjava r-summarizedexperiment)) (native-inputs - (list r-knitr zip)) ;zip is needed for repacking the jar + (list r-knitr r-testthat zip)) ;zip is needed for repacking the jar (home-page "https://bioconductor.org/packages/debCAM") (synopsis "Deconvolution by convex analysis of mixtures") (description @@ -5357,13 +6411,13 @@ knowledge can achieve semi-supervised deconvolution of mixtures.") (define-public r-decipher (package (name "r-decipher") - (version "3.0.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "1bgzl3sy4l5xfgxrkw8z1dvygkn2dgcl2fl9ah13ggs8hc9h9nlm")))) + "18fvmlxch10pgl9lnyww2506r7jbjigx6h2agjsm9wn5bga4mqzm")))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-dbi r-iranges r-s4vectors r-xvector)) @@ -5451,16 +6505,18 @@ mechanism based on the shared signatures.") (define-public r-decomptumor2sig (package (name "r-decomptumor2sig") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decompTumor2Sig" version)) (sha256 (base32 - "1pnxnxz9zsxqs7cbxgkjapr57k2m1d57w5hak0dwcy5zcxjzmai8")))) + "1ixasxw98ymj793sd2crm0jdg73jmy535xhss5dws156mhzl4y0f")))) (properties `((upstream-name . "decompTumor2Sig"))) (build-system r-build-system) - (inputs (list perl)) ;script/extractSpecColumns.pl + ;; This package installs Perl scripts: extractSpecColumns.pl, + ;; filterLines.pl, and filterLinesNumeric.pl. + (inputs (list perl)) (propagated-inputs (list r-biocgenerics r-biostrings @@ -5494,13 +6550,13 @@ of the signatures to the mutation load of the tumor.") (define-public r-deconrnaseq (package (name "r-deconrnaseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DeconRNASeq" version)) (sha256 (base32 - "0hwvfsc48dakh3nvz60i92yciz2m5my9w57kzpyj4jyk92cs181g")))) + "0v37kdv3cvh8s8ih5bk397k19b3fd4wldc7h0h8nyzv1z9lyal7v")))) (properties `((upstream-name . "DeconRNASeq"))) (build-system r-build-system) (propagated-inputs @@ -5521,13 +6577,13 @@ single expression profiles.") (define-public r-decontam (package (name "r-decontam") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decontam" version)) (sha256 (base32 - "1xjd9jzxlj6gfd6fnygzm21q1wy5x5pl031sq1q0svq3jlnzvgb7")))) + "0incm0dadkyn9n1k53cs19zgs3qc7y8hvfyq75vhqg670h4zyxkz")))) (properties `((upstream-name . "decontam"))) (build-system r-build-system) (propagated-inputs @@ -5547,13 +6603,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "181dxjj8bzy1b9xq9hd3m3ak1698w7j0sf8h9g0bhf3blzlj4pmi")))) + "1vl22cxrgfwixbrz40f0kq81ppybpv73fl8v14mfv6dp49pdkmml")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -5575,7 +6631,7 @@ negative control samples.") r-rsq r-s4vectors r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/BIMSBbioinfo/deconvR") (synopsis "Simulation and deconvolution of omic profiles") (description @@ -5592,13 +6648,13 @@ make mapping WGBS data to their probe IDs easier.") (define-public r-decoupler (package (name "r-decoupler") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "060ww5hlzk0dvh7a52i1nrz1s2xq5mmlw70rxpcs6d4j08k1cmic")))) + (base32 "0m7rmx64lhxg1l4qnx3ajp8w97nabp62r5mi4rfy0gh40n7z34i7")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs @@ -5615,7 +6671,7 @@ make mapping WGBS data to their probe IDs easier.") r-tidyr r-tidyselect r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://saezlab.github.io/decoupleR/") (synopsis "Computational methods to infer biological activities from omics data") (description @@ -5635,13 +6691,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "1rcq2bg4z6z7czqi662w5gsdc1vd4p8vb353hqayhciv31dz51fr")))) + "1prxiffyj2b7b7q5h2cc0w7ibzclm2wldqn0kcd66hqrmmcs7ypa")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -5671,13 +6727,13 @@ bases such as COSMIC.") (define-public r-degreport (package (name "r-degreport") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEGreport" version)) (sha256 (base32 - "0z5wzdixw6pyfd72drh54aalmp9nd5p1xi5vn53d58w78hrb757p")) + "01dhsr5lycr0mrcjgc3g4gb7sjpk6fdww3bl8w4fabqfpwkzz3d1")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "DEGreport"))) @@ -5724,6 +6780,7 @@ bases such as COSMIC.") (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) ("js-jquery-sticky-kit" ,(origin (method url-fetch) @@ -5744,16 +6801,19 @@ fold changes mean and variability for each selected gene.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.30.1") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0n6pparz2fg8wgrgcwciibqz3iyrnlmk5hdvnzjppcraxanz8sm6")))) + "12dbzjchx1f20i1va0fmh74xvn5pj84flnf0srmma2fma1i4rszy")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) + ;; Tests require r-hdf5array, but adding it would lead to a dependency + ;; cycle. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocgenerics r-iranges @@ -5779,13 +6839,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-densvis (package (name "r-densvis") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "densvis" version)) (sha256 (base32 - "1xsafzcg6psb4ld7nk4wgdaa3xhy8i2v86asasf8h3mi1ms7lcv0")))) + "0acqdhi13ihv9bxr2n5gh8ysk0ciak273pj495qr3s1pd8qz8772")))) (properties `((upstream-name . "densvis"))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -5794,7 +6854,7 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), r-rcpp r-reticulate r-rtsne)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/densvis") (synopsis "Density-preserving data visualization via non-linear dimensionality reduction") @@ -5814,15 +6874,26 @@ heterogeneity in the original high-dimensional space.") (define-public r-derfinder (package (name "r-derfinder") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinder" version)) (sha256 (base32 - "1i4m20wb08zncksz415jl8bd5r4gdygk7324cp6xhijrc1pfzl1i")))) + "0qg1klbb4g8nw7v50xb0p022barlspwaisdymyk12a04vd9q4i79")))) (properties `((upstream-name . "derfinder"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests attempt to download files. + (delete-file "tests/testthat/test_data.R") + ;; One test fails with: object of type 'closure' is not + ;; subsettable + (delete-file "tests/testthat/test_Fstats.R")))))) (propagated-inputs (list r-annotationdbi r-biocgenerics r-biocparallel @@ -5839,7 +6910,8 @@ heterogeneity in the original high-dimensional space.") r-rsamtools r-rtracklayer r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-derfinderdata r-knitr r-testthat + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://github.com/lcolladotor/derfinder") (synopsis "Annotation-agnostic differential expression analysis of RNA-seq data") @@ -5860,19 +6932,19 @@ The DER Finder approach can also be used to identify differentially bounded (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "0186wjrszf6c5amibmdblabx3cfvq7p7k6kza38gahw0p7ibwv21")))) + (base32 "0cs0m5ng6m932qsdzmi8rv2p3wc0d6hx17n75srgjbm4cdq70q8h")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs (list r-iranges r-matrix r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/leekgroup/derfinderHelper") (synopsis "Helper for derfinder") (description @@ -5885,13 +6957,13 @@ calculation in parallel.") (define-public r-dmrcate (package (name "r-dmrcate") - (version "3.0.8") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DMRcate" version)) (sha256 (base32 - "1j3s3lcsfwywyaaifiyz1pl9wd8s5wbdwjx71827wz346gpppkbv")))) + "0diky1jam8k1b61xkwaxbsx6pd599d1pf0xw9s7yr17fm4rbqhm9")))) (properties `((upstream-name . "DMRcate"))) (build-system r-build-system) (propagated-inputs @@ -5910,7 +6982,7 @@ calculation in parallel.") r-plyr r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/DMRcate") (synopsis "Methylation array and sequencing spatial analysis methods") (description @@ -5926,13 +6998,13 @@ possibly confounded by SNPs and cross-hybridisation. It includes (define-public r-drimseq (package (name "r-drimseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "10skx3n3r9vp1p1499ddccgabi7q3cy1dpi5pbp4ap0gff5ika5x")))) + (base32 "0bfchi7igh21ifjjim59lwbql69gcddl39imxh49w2hv7pr3227w")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs @@ -5946,7 +7018,7 @@ possibly confounded by SNPs and cross-hybridisation. It includes r-mass r-reshape2 r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/DRIMSeq") (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") (description @@ -5961,13 +7033,13 @@ results.") (define-public r-dropletutils (package (name "r-dropletutils") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DropletUtils" version)) (sha256 - (base32 "01y88cnii02sn1jgyvvmbx8j60qbzqyznqfxzv06yi4y0xj37klg")))) + (base32 "0659hpzjcch68dwi73a9rnkbxxfvivd09208z60q2fd22w2qgdjx")))) (properties `((upstream-name . "DropletUtils"))) (build-system r-build-system) (propagated-inputs @@ -5990,8 +7062,9 @@ results.") r-s4vectors r-scuttle r-singlecellexperiment + r-sparsearray r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/DropletUtils") (synopsis "Utilities for handling single-cell droplet data") (description @@ -6016,7 +7089,7 @@ pseudo-cells, and downsampling of the count matrix.") (properties `((upstream-name . "dsb"))) (build-system r-build-system) (propagated-inputs (list r-limma r-magrittr r-mclust)) - (native-inputs (list r-knitr r-rmarkdown)) + (native-inputs (list r-knitr r-rmarkdown r-testthat)) (home-page "https://github.com/niaid/dsb") (synopsis "Normalize & denoise droplet single cell protein data (CITE-Seq)") @@ -6034,13 +7107,13 @@ in Python.") (define-public r-dss (package (name "r-dss") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 - "1y9xg6ic3a03xswyfvyxdhnd7ngkljc96bm5fry4ni6kpa77bkv8")))) + "03dzxxlyqymp827w2sdrpwn51q8n5xggx06m8gh7p1aigk5c50ah")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) @@ -6060,13 +7133,13 @@ Beta-Binomial distributions.") (define-public r-dyndoc (package (name "r-dyndoc") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DynDoc" version)) (sha256 (base32 - "174jfdyq7g7mvn7wvmdkf36n0n969aqsg9bwd1nk6a5nw1khm7js")))) + "0pz2sz99p5dqprfwhnh22mw9j8895jk1gm3ffqysq7afim2fla5m")))) (properties `((upstream-name . "DynDoc"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DynDoc") @@ -6079,17 +7152,18 @@ dynamic documents and vignettes.") (define-public r-bluster (package (name "r-bluster") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1bj7wx2dnwbrv2gxcmqmq815vawfiqj2xy3624fjli11r8c1hywa")))) + "1k8aj5zj297l5yf15f3xak9adcrxr79ax7ifwhz2jq23ifd4dmfs")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs - (list r-biocneighbors + (list r-assorthead + r-biocneighbors r-biocparallel r-cluster r-igraph @@ -6097,7 +7171,7 @@ dynamic documents and vignettes.") r-rcpp r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/bluster") (synopsis "Clustering algorithms for Bioconductor") (description"This package wraps common clustering algorithms in an easily @@ -6109,13 +7183,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "0mq8qdhi2ccfa66rygn83hpm0fsmwiahpmrh8q522yl618mkrjcs")))) + "0n4q519x6fndz68w7zd0naw7cdrricxsvd2cqwc6y05w11jk34f3")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -6133,15 +7207,17 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "1fi89fqzzb9n2c9jchkkgy3yq2fvisjcdavh9r455vmy0xqsyyyd")))) - (properties `((upstream-name . "infercnv"))) + "04ccxn2nzwjmcpbsxrksavrhjgbwv1zpc9i9dkyjsf0sirhn1mkf")))) + (properties + `((upstream-name . "infercnv") + (updater-extra-inputs . ("python")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs @@ -6176,7 +7252,7 @@ arbitrary genomic intervals along chromosomal ideogram.") r-singlecellexperiment r-summarizedexperiment r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/broadinstitute/inferCNV/wiki") (synopsis "Infer copy number variation from single-cell RNA-Seq data") (description @@ -6193,16 +7269,18 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.38.1") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "07q9j00rvgdbv582p01nxc99j0gfx4fsarpl1w1fjx5nb8y86k4v")))) + "1mvlm8xkrrfp5m9d2ar0kl9m4hgr05xmmys33dq5zwrzi5idqp0y")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) + ;; Some tests require r-xvector, causing a dependency cycle. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocgenerics r-s4vectors)) (home-page "https://bioconductor.org/packages/IRanges") @@ -6221,13 +7299,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "0mmxyq1r4kq1igj108pr0r9215hwmyph5svx0djd460knak24y6z")))) + (base32 "13vp30mgf0v604i4vxbklbq1fh0wwn15gk05dvm7lpf5zppaqvgd")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs @@ -6303,13 +7381,13 @@ AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).") (define-public r-italics (package (name "r-italics") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICS" version)) (sha256 - (base32 "06h6iqrqzlcj4hyhj1ikl9isr3ls1pph49v5n7cp87czinr0nd3s")))) + (base32 "1wvyqp0fji0hhshr4y1fwqjy6vlqgdrnj7is9glbvvjb9505rzp1")))) (properties `((upstream-name . "ITALICS"))) (build-system r-build-system) (propagated-inputs @@ -6371,7 +7449,7 @@ absolute GSEA.") (propagated-inputs (list r-biobase r-limsolve)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type @@ -6438,13 +7516,13 @@ mapping.") (define-public r-nebulosa (package (name "r-nebulosa") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Nebulosa" version)) (sha256 (base32 - "0m5z6rribsrk9mzcksjh0nmpf4d0x0hn8jd80h0hj0hj8sj1ifgv")))) + "15bdddc34y6i1j06fpi82p8xz07p4q07p2js657gssh4lwxkz5n1")))) (properties `((upstream-name . "Nebulosa"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -6455,7 +7533,7 @@ mapping.") r-seuratobject r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/powellgenomicslab/Nebulosa") (synopsis "Single-cell data visualisation using kernel gene-weighted density estimation") @@ -6546,7 +7624,7 @@ Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.") r-stringr r-synchronicity)) ;suggested (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description @@ -6561,15 +7639,17 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "19z22c1yd3rkwk7dp8q8xv16n0qv92iz00vzid3pniy7zr80cxxy")))) + "1x27cbqsip5m7lzv5nvffdfjp46cdqh53qb1xvi2rf0wfdnd7763")))) (build-system r-build-system) + ;; Some tests require r-affydata, causing a dependency cycle. + (arguments (list #:tests? #false)) (propagated-inputs (list r-affyio r-biobase @@ -6589,14 +7669,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "02n2v1iwkhmilv1bjfza2yrqj7rsr8v46bghajcb8wdyyaj759ib")))) + "10z63g0vj8c7gnzqi3dpx543idyp2fa6majs2ydv41jah6s10zs2")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -6655,14 +7735,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0r4pqda9pv60b867c6yi328687kyxjglk5jmcal6xnlr75nf4w0y")))) + "0vsh2qazn8zjy9k7ha59krv4psmzl6cvka68h8gkz6xj38f9kxjw")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -6678,14 +7758,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "0w138n3f68ndr0innk981vf8p5wb729m31p0d3f9qp08hmv58jfw")))) + "1xyanwj6psrqqj2m5rb0p3890m7kddkj7gnbllknbbib1jjh24rf")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -6720,14 +7800,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "156sijj9zy01p038m7yw58h1bw1ii0kd5q9kv3krh6bs67c3dv8h")))) + "01asrih2ish0l2yr0g6azbsn23cf8f3fc4ks8rn6w1rc054405ci")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) @@ -6744,14 +7824,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0qqc2sq331g2ml390nhjkrnldp6bi7r6xyz7rw77hnr3qpcrhqk2")))) + "1b68jnl1w9lk3z20774dlhj98fb4hfjkq3y8pv4gbz4kkgy44a6f")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -6772,15 +7852,17 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "1v4sq22lwrhl50whag0jil788wwvi4rpdaij03iwak93q998ls0f")))) + "1m7cc5hawzdvm0b1il4fcilipnsv1n94zqvwhkbr3041rklf7l7y")))) (build-system r-build-system) + ;; Tests require a number of annotation packages. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-biobase @@ -6789,6 +7871,7 @@ structure.") r-httr r-xml r-xtable)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/annotate") (synopsis "Annotation for microarrays") @@ -6799,16 +7882,18 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1g2yzbx7djkk8kccbclxv953iijmjvsjsalfv1ihmmcai33979rs")))) + "13gqbmx7pqnl6g087kz1isnw61jbljq8pizzn5wf4hv9c76dlvpf")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) + ;; Tests require annotation packages that depend on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biobase r-biocgenerics @@ -6829,20 +7914,20 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "1sdm85sl4d9mqbjgjh3yizcmrzgz0g4x17s25gss2f6cjwy5jp40")))) + "1a7ffcxdx95irbcr2sh7sph6x5lf7spnyq084pvx9qd18i6cif5n")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) (propagated-inputs (list r-genomicranges r-lazyeval)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/Bioconductor/AnnotationFilter") (synopsis "Facilities for filtering Bioconductor annotation resources") (description @@ -6854,14 +7939,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1ikri9hb1s0jzw1wyfpwsl02hg8dw2xs703sp085sbsq3cwk9cn1")))) + "1m3s3jkq43w94mr4g3cqfgndan7ihhhnx84ag4xm1rzmvdpsd0pp")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -6875,7 +7960,7 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") r-s4vectors r-xml)) (native-inputs - (list r-knitr)) + (list r-go-db r-knitr r-runit)) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description @@ -6886,16 +7971,18 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "1da2n13j2xysnd175zi7s6zm8yllnp0k59vygkx9id85jcldqf51")))) + "1l0wjc6kapkvj047g11755ardsg12jmlmvb6bq3jvp34ida7j8in")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) + ;; Many tests try to download files. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-biocfilecache @@ -6910,7 +7997,7 @@ databases. Packages produced are intended to be used with AnnotationDbi.") r-s4vectors r-yaml)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -6926,18 +8013,19 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1v24b43knsjpw44zkrzv8pvxjiw12rcz9wqp4ahd88dg23j7pvwz")))) + "0n92bmjm97kzv2lpkkc2d4lgs7nzqwrcijq2j4v53xawbcgdxcfd")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils)) + (native-inputs (list r-princurve)) (home-page "https://github.com/HenrikBengtsson/aroma.light") (synopsis "Methods for normalization and visualization of microarray data") (description @@ -6950,14 +8038,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "1jq993m6b0cv3ibgjrbzyka7svb653hvi6bvqhf8ir3lgjgs23dp")))) + "1cp4wh9w12vw7iq5cj3v4nh99md1bizrnw312sgib2r3x4p6vpf6")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -6967,7 +8055,7 @@ classes.") r-rhtslib r-zlibbioc)) (native-inputs - (list r-knitr)) + (list r-knitr r-rsamtools r-testthat)) (home-page "https://bioconductor.org/packages/bamsignals") (synopsis "Extract read count signals from bam files") (description @@ -6980,16 +8068,18 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "09xnl0qq4qsd981i9srw07228lgashcvcavi8k0izdzfyk6ka7m2")))) + "1ndkvl44pxdsw39gka1ivlb8l89m1ix58nkji7b65qq9mj6dw31k")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) + ;; One test depends on golubEsets, which depends on r-biobase. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocgenerics)) (native-inputs (list r-knitr)) @@ -7003,19 +8093,34 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.60.1") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0mzdxpagxwiwyznhd7h93cgy01a2j85rgb5dpnkzgp4sxw01n7rb")))) + "16xh2vj729sjg9660w1sw5jcz59sawbni3i2nf8rzawaqf0ks979")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests attempt to download files. + (for-each delete-file + '("tests/testthat/test_ensemblFunctions.R" + "tests/testthat/test_ensemblGenomes.R" + "tests/testthat/test_getBM.R" + "tests/testthat/test_z_cache.R" + ;; This produces unexpected warnings. + "tests/testthat/test_ensembl_ssl_settings.R"))))))) (propagated-inputs (list r-annotationdbi r-biocfilecache + r-curl r-digest r-httr2 r-progress @@ -7023,7 +8128,7 @@ on Bioconductor or which replace R functions.") r-stringr r-xml2)) (native-inputs - (list r-knitr)) + (list r-httptest2 r-knitr r-mockery r-testthat)) (home-page "https://bioconductor.org/packages/biomaRt") (synopsis "Interface to BioMart databases") (description @@ -7070,7 +8175,7 @@ powerful online queries from gene annotation to database mining.") r-tibble r-withr r-xml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/biomartr/") (synopsis "Genomic data retrieval") (description @@ -7087,19 +8192,20 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1miw26r2a8wvgnfr9sapfv6rqk219rmsyjh6v04annafxdxy15ky")))) + "1avnn7xpcabw73w75x66fxlx8wmlmv69p1zmr493gbgvy85plv1z")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'make-reproducible (lambda _ ;; Remove generated documentation. @@ -7126,7 +8232,7 @@ only one command.") (propagated-inputs (list r-bh r-codetools r-cpp11 r-futile-logger r-snow)) (native-inputs - (list r-knitr)) + (list r-batchtools r-biocgenerics r-doparallel r-knitr r-runit)) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -7138,13 +8244,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.72.1") + (version "2.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "067vy2v7spbdsknvi0fcpdi085kn8v20pyrhkc7wy357v21h7hgs")))) + "1z50mmp34rpl9mr571g1whvfnxlcnk196k9naxjngl0qriyymcvl")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7155,7 +8261,7 @@ objects.") r-iranges r-s4vectors r-xvector)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/Biostrings") (synopsis "String objects and algorithms for biological sequences") (description @@ -7167,14 +8273,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1jbcnjjwdjy7zfy0ybgfy1y5ym7rygzkailr5bm4hnh9bn2837p7")))) + "0g4hh3ka9891yamf90y1964xn7qsgzqwnb3f0dsmqbmbryk8pyz6")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -7197,6 +8303,7 @@ biological sequences or sets of sequences.") r-scales r-summarizedexperiment r-variantannotation)) + (native-inputs (list r-ensdb-hsapiens-v75 r-runit)) (home-page "https://bioconductor.org/packages/biovizBase") (synopsis "Basic graphic utilities for visualization of genomic data") (description @@ -7209,13 +8316,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1pjbkakrycvaifl7xrmri2h94zc1ap8a9d1q4c83qji3xa21cm4q")))) + "0abcz2rpw9af2cfyssz6adbx36issjlwzf7ipj1vkcmia6j5f1ji")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -7231,6 +8338,7 @@ effort and encourages consistency.") r-rtracklayer r-s4vectors r-xvector)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/BSgenome") (synopsis "Infrastructure for Biostrings-based genome data packages") (description @@ -7241,16 +8349,28 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.70.0") + (version "2.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0paz6h8rsbqvlxxj4di8cl76aybgjr842z5gdv8xi6c2d7zwbclw")))) - (properties `((upstream-name . "Category"))) + "0s65rfk9sw02qdqk7jhbkjybx1sm0hq0impdcxyypxbg77db5wk2")))) + (properties + `((upstream-name . "Category") + (updater-ignored-native-inputs . ("r-gostats")))) (build-system r-build-system) + (arguments + (list + ;; Vignettes attempt to connect to rest.kegg.jp. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests need r-gostats, which depends on this package. + (delete-file "inst/UnitTests/hyperGTest_test.R")))))) (propagated-inputs (list r-annotate r-annotationdbi @@ -7262,6 +8382,16 @@ genome data packages and support for efficient SNP representation.") r-gseabase r-matrix r-rbgl)) + (native-inputs (list r-all + r-geneplotter + r-hgu95av2-db + r-karyoploter + r-keggrest + r-lattice + r-limma + r-org-sc-sgd-db + r-rcolorbrewer + r-runit)) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description @@ -7272,13 +8402,13 @@ analysis.") (define-public r-champ (package (name "r-champ") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChAMP" version)) (sha256 (base32 - "06q539yhbmbp7qr71cwjai2vdw5nnhhjdv2ajlqmlyjpg04arc7v")))) + "0cbgzkza1gqrqyk32i9vy1s3qvvr0wx2j0fjwg1cqy42qdy24rax")))) (properties `((upstream-name . "ChAMP"))) (build-system r-build-system) (propagated-inputs @@ -7334,16 +8464,16 @@ regions and to highlight copy number alterations.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "00iknjk7vgj48vj1pp7l98g7nvc3x495z3jcq5nbvdiff02faj1f")))) + "0l15apga9c0pcclvdx4zdyl9zd3v4isc5rb95d7h7s2wa3mskaxh")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (propagated-inputs (list r-annotationdbi r-aplot @@ -7360,8 +8490,11 @@ regions and to highlight copy number alterations.") r-iranges r-magrittr r-plotrix + r-rcolorbrewer + r-rlang r-rtracklayer r-s4vectors + r-scales r-tibble r-txdb-hsapiens-ucsc-hg19-knowngene r-yulab-utils)) @@ -7381,14 +8514,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1rd56knaf0ar8d0nh0mcnrrg5jy0csixig1d4abn1b64vbzrvzpz")))) + "0s50i1dzbqwdxb6zn8v4ip2n6r3dmkgahx5kjixpi45s42d8yn31")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -7408,14 +8541,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1ppzx850nvvdhz2xiggr43c79w0nr0vmsmmnszasd4flf3jm7v8v")))) + "1hab197h1d01p8960zqmb0vnhgw9bk68ibmappryhv1jb4ibmx60")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -7434,7 +8567,7 @@ experiments.") r-png r-rcolorbrewer)) (native-inputs - (list r-knitr)) + (list r-dendextend r-genomicranges r-gridtext r-knitr r-testthat)) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -7483,6 +8616,7 @@ self-defined annotation graphics.") r-rlang r-rtsne r-sccore)) + (native-inputs (list r-pagoda2 r-testthat)) (home-page "https://github.com/kharchenkolab/conos") (synopsis "Clustering on network of samples") (description @@ -7570,14 +8704,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1j7ivkxbc75hzxhl9d97w8vamrmxf6527n7841i1j9n6s7hz1cdn")))) + "0n0cq388rds9x8nxy13srzhm3sc0x539xb26nn1bz05c177kmwxb")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -7595,7 +8729,7 @@ distribution.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr r-rmarkdown)) + (list r-knitr r-rmarkdown r-testthat)) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -7608,14 +8742,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "13y3fhgvf7438yjv6qm28n8f42w4wgkklc0q229ypns1gfh54524")))) + "05sjxxv5299m0i9hnhz037dz6f5q8qdb70vbvr28jjzc1jcv7ym8")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -7637,7 +8771,7 @@ distribution.") r-stringr r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/DEXSeq") (synopsis "Inference of differential exon usage in RNA-Seq") (description @@ -7653,13 +8787,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "1iyqvang5j55s19skd44c1zsxkphn3qqbl4sjhsw1y820ylws5r1")))) + (base32 "0vjd0c9zql6w9iyp8fsr3rqwx4lybn8yfk421p8wgg29nlpg8zk6")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -7677,7 +8811,7 @@ exploration of the results.") r-s4vectors r-summarizedexperiment r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/lmweber/diffcyt") (synopsis "Differential discovery in high-dimensional cytometry") (description @@ -7691,14 +8825,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0djd84vnf4skjr6m25ykqrvwa37lgs5r5aw9md81ykaqmi40szqb")))) + "1chwd1zidc0abjl4kc5j58f4dwbghwnzlqx47ymln35b2gggj61w")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -7706,6 +8840,7 @@ adapted from transcriptomics.") (list gsl)) (propagated-inputs (list r-biocgenerics r-iranges r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DirichletMultinomial") (synopsis "Dirichlet-Multinomial mixture models for microbiome data") (description @@ -7718,13 +8853,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "15p01f3yaan9x7y6ld1kx40jnbcn6vjjm5n6ir7cicdvv4w5ln49")))) + "0c38wq57kpm7pjsca2kpyr2rmk37wak66d57mxsd6bwxmqzsys2r")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -7739,7 +8874,15 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): r-s4vectors r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-complexheatmap + r-deseq2 + r-edger + r-ggplot-multistats + r-ggrastr + r-knitr + r-plotly + r-testthat)) (home-page "https://bioconductor.org/packages/dittoSeq") (synopsis "Single-cell and bulk RNA sequencing visualization") (description @@ -7762,14 +8905,14 @@ code{dittoColors()}.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "18h9zlah21lghy1sjpnzy6lddmff8vh3raxnqi15v00za9azk8yq")))) + "1k061w169p8r71xq4ss2hda7k2p38h8pxcggfpjfii57wb3mvdk0")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -7786,7 +8929,7 @@ code{dittoColors()}.") r-rsamtools r-shortread)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -7802,17 +8945,17 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.2.1") + (version "4.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0c9r4gcsaf6fqkc4r49vj8az6wplqsbkd423pb4fvrv5lka9aqi9")))) + "0h6iks08n5ha1fxqxzcy35qj697k4i0mjlklpq7rd6xpaigy64k7")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs - (list r-limma r-locfit r-rcpp)) + (list r-limma r-locfit)) (native-inputs (list r-knitr)) (home-page "https://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") @@ -7828,17 +8971,17 @@ CAGE.") (define-public r-enhancedvolcano (package (name "r-enhancedvolcano") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnhancedVolcano" version)) (sha256 (base32 - "0ry5r74d6m5x15b4azw93mjrvq4fapj4rxpi9f6macz4l5l6j1j0")))) + "16z9117cgggq1dn9fymq39wbsjlhn2dvwqh69kzhf7cg79b2czap")))) (properties `((upstream-name . "EnhancedVolcano"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrepel)) - (native-inputs (list r-knitr)) + (native-inputs (list r-biocgenerics r-knitr r-runit)) (home-page "https://github.com/kevinblighe/EnhancedVolcano") (synopsis "Publication-ready volcano plots with enhanced coloring and labeling") @@ -7856,13 +8999,13 @@ parameter configurations.") (define-public r-enmix (package (name "r-enmix") - (version "1.40.2") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ENmix" version)) (sha256 (base32 - "1x8rzdzymibypb65axx3sgxsgrj5d1fldj9j70acvg46lqhmq8f2")))) + "1p0x2jq327r0lsnq1wdy19w5bsa4kvkhj5b6cr1dy1sgdxa7n4wr")))) (properties `((upstream-name . "ENmix"))) (build-system r-build-system) (propagated-inputs @@ -7886,7 +9029,7 @@ parameter configurations.") r-rpmm r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-minfidata r-runit)) (home-page "https://bioconductor.org/packages/release/bioc/html/ENmix.html") (synopsis "Quality control and analysis tools for Illumina DNA methylation BeadChip") @@ -7898,15 +9041,18 @@ visualization of Illumina DNA methylation array data.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.28.1") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0gfwz7gznxpnqis7ack3106gvpbhcarlmj41ivndxzvksnxc3yq1")))) + "1p7hlhyzirzcq1g0i62hr3l4k60fm4y04qb4k04lls8wynfxhy0a")))) (build-system r-build-system) + ;; The tests require r-ensdb-hsapiens-v86, which depends on + ;; this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-annotationfilter @@ -7943,13 +9089,13 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-epidish (package (name "r-epidish") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EpiDISH" version)) (sha256 - (base32 "17qkm5inavfdfrim9baqxdhs3w64c6y94qadw4y5p9xsck318frq")))) + (base32 "1az3paxj20bkp75q71lprdsws4vya6bwgjsw6nxx8j4rpd8jz8hn")))) (properties `((upstream-name . "EpiDISH"))) (build-system r-build-system) (propagated-inputs (list r-e1071 @@ -7959,7 +9105,7 @@ chromosome region or transcript models of lincRNA genes.") r-matrixstats r-quadprog r-stringr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/sjczheng/EpiDISH") (synopsis "Epigenetic dissection of intra-sample-heterogeneity") (description @@ -7974,14 +9120,14 @@ their directionality of change in Epigenome-Wide Association Studies.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "03gl7z7q90jy47q57gfbj5fkv5n8hi43jbbrl53bdyp71f26ry2d")))) + "1yjpn8qi3q7cc7hqrqpa5nnjd7r0nrahnqgxv2kzk85klkpiyq5f")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges @@ -8002,14 +9148,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0iwdv9y5x0na38arjqacz00s7plk7aqc1h2ynhlpbyl3nz0a0kyq")))) + "06kd8cklhqp8w2iqli427k072wg0z2hd08y8c61ds5rkqhk7m13d")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -8030,14 +9176,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.86.0") + (version "1.88.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0jp7jvgzb1bs0p76j9k8lhgliipjnif6bng7hdn5wi744jb5fmpr")))) + "1c5mi7g5l501x8l0cd27cvqpwfki740yxj9598sgvgmd8v8aczyd")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -8054,16 +9200,17 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "0bfd4322m6g7dvas214i17k8sjsf62lza9darmhiwb4r8h30qmb2")))) + "05ca6g9qxkhb55b7bcr449xa0x4qdixxyx1y2d5kn0xj2zcy3lp9")))) (build-system r-build-system) (propagated-inputs (list r-gplots r-rcolorbrewer)) + (native-inputs (list r-biocgenerics r-biocstyle r-runit)) (home-page "https://www.bioconductor.org/packages/GeneOverlap/") (synopsis "Test and visualize gene overlaps") (description "This package can be used to test two sets of gene lists @@ -8073,13 +9220,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1bfy46kka77q93s42hsbxpiynfkin5mh7cz3w592smw2dzkh01j4")))) + "17vwkw85936hdxw503gjd4l7js5pzv9zvcscvmhaasnfck1l9y48")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -8103,7 +9250,7 @@ and visualize the results.") r-s4vectors r-seqpattern)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description @@ -8120,16 +9267,18 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "155wj17pbdbixyg6mimv06wg3ylll8ysqh7rffjp65fw662jwhw0")))) + "070llxf6qv3yhs46riff02myghb4gni8510dppdcbfizg0mf41ba")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) + ;; Tests attempt to download files. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocgenerics r-genomeinfodbdata r-iranges r-s4vectors r-ucsc-utils)) @@ -8147,16 +9296,18 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "15jzdjna0r9n6ybvyw52v1d9f05vdsdxff0g8q0pa584a1sd2s7s")))) + "1ycawwp0b8gk9sccqdwklq4yh3rns9iw34qdx5ysw4nxksi4vf6y")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) + ;; Vignettes require more packages. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-biocgenerics r-biocparallel @@ -8167,6 +9318,7 @@ names in their natural, rather than lexicographic, order.") r-rsamtools r-s4vectors r-summarizedexperiment)) + (native-inputs (list r-knitr r-pasillabamsubset r-runit)) (home-page "https://bioconductor.org/packages/GenomicAlignments") (synopsis "Representation and manipulation of short genomic alignments") (description @@ -8180,28 +9332,37 @@ alignments.") (define-public r-genomicdatacommons (package (name "r-genomicdatacommons") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicDataCommons" version)) (sha256 (base32 - "0jg4sa1lqn028y2ympb3x4s8yr7qa8ajrwqj2hhcl8zss3sx8gr2")))) + "1vw4lsh3bkmghk4f5rqds0awvl0f5dkafz51iw3s6lqaviq5wkx3")))) (properties `((upstream-name . "GenomicDataCommons"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests attempt to download files. + (for-each delete-file + '("tests/testthat/test_api.R" + "tests/testthat/test_data.R"))))))) (propagated-inputs (list r-dplyr r-genomicranges r-httr r-iranges r-jsonlite - r-magrittr r-rappdirs r-readr r-rlang r-tibble r-tidyr r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/GenomicDataCommons") (synopsis "NIH/NCI genomic data commons access") (description @@ -8212,16 +9373,18 @@ Commons RESTful service.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1r1d9g5vq5y946v2z2xgmfb31k0576nj8i0yg6xfj9y2a0a6akc5")))) + "0ixc6hmfdh2dn985d92iwcmk2v5m1c2l3d27y76bzmw9whpd89i5")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) + ;; Test require r-txdbmaker, which depends on r-genomicfeatures. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-biocgenerics @@ -8251,14 +9414,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1b0n5aqvg6jb6rpikjzxndmcjxp31h6vhr1magzalqg7jmlvcv6i")))) + "0vfk4nxdgvh57swcf9p898cli7v3i8c6q4aw9qr5sjv01kxr51rg")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -8274,7 +9437,7 @@ extracting the desired features in a convenient format.") r-s4vectors r-summarizedexperiment r-variantannotation)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/GenomicFiles") (synopsis "Distributed computing by file or by range") (description @@ -8286,20 +9449,22 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.56.1") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0g0ld9i58pdxw2pwxi9nzj82mkryag457pvh6cvbvhb28pfamkma")))) + "1iccjn5gb8k2l1hw7nhi30w3dnlpdf8mh3xwf3x3dky3mhxw3j0h")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) + ;; The vignettes require more packages. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector)) (native-inputs - (list r-knitr)) + (list r-biostrings r-biocstyle r-knitr r-runit)) (home-page "https://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") (description @@ -8313,13 +9478,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-glad (package (name "r-glad") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GLAD" version)) (sha256 (base32 - "01qn4v7b7b633dz01njzmg48lga861pfqnys9f0fbk9damxc6rr1")))) + "05vn4zmazkkf0m3shm08dkwlb8whwqqw0vr5h27vlxlz3bcjnqcf")))) (properties `((upstream-name . "GLAD"))) (build-system r-build-system) (inputs (list gsl)) @@ -8337,13 +9502,13 @@ regions identified.") (define-public r-globalancova (package (name "r-globalancova") - (version "4.22.0") + (version "4.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GlobalAncova" version)) (sha256 (base32 - "0z71a5h4y740k0hx84aavfxl1kpshm4gqs7mh6zf895i2r761bqh")))) + "1hxggdicpqhwyai53sa20y63dmn48rlys56iyk1rwnxwd8dsmjn0")))) (properties `((upstream-name . "GlobalAncova"))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -8369,13 +9534,13 @@ linear models via the extra sum of squares principle.") (define-public r-globaltest (package (name "r-globaltest") - (version "5.58.0") + (version "5.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "globaltest" version)) (sha256 (base32 - "1cpvs1jcp9ibis06pkbqvhhksy6cis0zynx774d0hqdbb9ljl945")))) + "1gi62ynkyvrzi6m691206wrlprid028h1rj1p725k4myi5fh06jr")))) (properties `((upstream-name . "globaltest"))) (build-system r-build-system) (propagated-inputs @@ -8393,14 +9558,14 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.") (define-public r-gostats (package (name "r-gostats") - (version "2.70.0") + (version "2.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1dygsr8nlqksfpk00lk67dhj4fcpjg1x4dbl2r4sfanlk4hq76cs")))) + "0zz2gmv2hg8cr0bxj4zb95p8cf8a19zx1v925cv5f4xh7m698bzj")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -8413,7 +9578,7 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.") r-graph r-rbgl r-rgraphviz)) - (native-inputs (list r-knitr)) + (native-inputs (list r-biocgenerics r-hgu95av2-db r-knitr r-runit)) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") (description @@ -8425,14 +9590,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1pnd8rmpk7gm89cvrqa8qwk40dszkfkhyydxp3gl13zng9c5bq40")))) + "0zd37jpx2zy9gxl3b2vkr7m2fq8xm1pcxk352dw3mlv1gadhsz9n")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -8443,7 +9608,13 @@ testing and other simple calculations.") r-graph r-xml)) (native-inputs - (list r-knitr)) + (list r-go-db + r-hgu95av2 + r-hgu95av2-db + r-knitr + r-org-hs-eg-db + r-runit + r-testthat)) (home-page "https://bioconductor.org/packages/GSEABase") (synopsis "Gene set enrichment data structures and methods") (description @@ -8454,18 +9625,19 @@ Enrichment Analysis} (GSEA).") (define-public r-gsva (package (name "r-gsva") - (version "1.52.3") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GSVA" version)) (sha256 (base32 - "08nxg3q350n5gf975r6b0zq4cr7lchv2i811crc4xbb7q39kw8k4")))) + "0f183wz2rzrdxhkaz9c1q1przbg5wqp6fygsba2xszqmi026dppr")))) (properties `((upstream-name . "GSVA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-biocsingular + r-cli r-delayedarray r-delayedmatrixstats r-gseabase @@ -8477,7 +9649,7 @@ Enrichment Analysis} (GSEA).") r-sparsematrixstats r-spatialexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-gsvadata r-knitr r-runit)) (home-page "https://github.com/rcastelo/GSVA") (synopsis "Gene Set Variation Analysis for microarray and RNA-seq data") (description @@ -8495,17 +9667,19 @@ manner.") (define-public r-gypsum (package (name "r-gypsum") - (version "1.0.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gypsum" version)) (sha256 - (base32 "1zrmxmlnbiifc2p5mn10y3vpmyzqjimd2hvc3s9c0j0iv6ryxjv0")))) + (base32 "1qyb90r5qji9r0hy986891dyjqmryyszjp2v27q054mimwbgwskk")))) (properties `((upstream-name . "gypsum"))) (build-system r-build-system) - (propagated-inputs (list r-filelock r-httr2 r-jsonlite)) - (native-inputs (list r-knitr)) + ;; Some tests need internet access. + (arguments (list #:tests? #false)) + (propagated-inputs (list r-filelock r-httr2 r-jsonlite r-rappdirs)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ArtifactDB/gypsum-R") (synopsis "Interface to the gypsum REST API") (description @@ -8520,13 +9694,13 @@ details.") (define-public r-harshlight (package (name "r-harshlight") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Harshlight" version)) (sha256 (base32 - "1nqi2ad9hnm6j8hn8f6xp9zav6rsa5wlzb2z5fjnm9q4xbjblnjl")))) + "14fnbvrk7cdfnsdv47cv1k4krqlf9a8hiax0m7g8rw1y7qjkf0z4")))) (properties `((upstream-name . "Harshlight"))) (build-system r-build-system) (propagated-inputs @@ -8547,14 +9721,14 @@ matrix to solve the memory problem.") (define-public r-hpar (package (name "r-hpar") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1qqa0p8k3h8pbbgfz9d1k08zml5i5r9iwi2xqqj1hg84n2saqkzp")))) + "0b3m2krlmvfjcwb0f6y5gxwdi55hizzps1cp7imgx1mqgsv5gjya")))) (build-system r-build-system) (arguments (list @@ -8572,7 +9746,7 @@ matrix to solve the memory problem.") "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}")))))))) (propagated-inputs (list r-experimenthub)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from @@ -8582,13 +9756,13 @@ the Human Protein Atlas project.") (define-public r-r3cseq (package (name "r-r3cseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "r3Cseq" version)) (sha256 - (base32 "02dc6milwymwj90x24fip8av84ik9dp69sg9g7l300kwyk0hcrb7")))) + (base32 "0siicyjr5zb9z1ymlasrnrvggcrnrpf9194s5qfhybasgai6a5jm")))) (properties `((upstream-name . "r3Cseq"))) (build-system r-build-system) (propagated-inputs @@ -8614,13 +9788,13 @@ interactions from 3C-seq assay.") (define-public r-r4rna (package (name "r-r4rna") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "R4RNA" version)) (sha256 - (base32 "0cpfngd11zlws756q8cnhy5451kj8hg5ckilvmhndfapkz4w93x1")))) + (base32 "0g0lrj5vs2dd3hgm5l0h91hrprzbg02cr5r3kyjqmmzfixr1rzqc")))) (properties `((upstream-name . "R4RNA"))) (build-system r-build-system) (propagated-inputs (list r-biostrings)) @@ -8637,13 +9811,13 @@ with numerical methods for computing statistics for each.") (define-public r-radiogx (package (name "r-radiogx") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RadioGx" version)) (sha256 - (base32 "0ykw5hm48fh6xqxdfgmjjbqdd5hp4dmhnykg3zkmb9wrcfp4zx7f")))) + (base32 "0lcsvbqcw7rf21d5gwis6n055r2j30qh0526j0im70vqyhp4928m")))) (properties `((upstream-name . "RadioGx"))) (build-system r-build-system) (propagated-inputs @@ -8682,13 +9856,13 @@ fraction} are included.") (define-public r-raggedexperiment (package (name "r-raggedexperiment") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RaggedExperiment" version)) (sha256 (base32 - "0xfg88r5nh0qswsfc3mm595jmf2w8s2dr032apd15b3kc40hjlr9")))) + "0np94bh1qxwwmllxsf2hf4vv7lnjmghrjfg1g07kcwfhnmm5n56l")))) (properties `((upstream-name . "RaggedExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biocbaseutils @@ -8700,7 +9874,7 @@ fraction} are included.") r-matrixgenerics r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/RaggedExperiment") (synopsis "Representation of sparse experiments and assays across samples") (description @@ -8716,16 +9890,17 @@ rectangular dataset.") (define-public r-rdisop (package (name "r-rdisop") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rdisop" version)) (sha256 (base32 - "1gcg441mp6bdnzjkh4gg6zgjn4hnw5i8mdcvb1hfim4hsc7sdsxv")))) + "04w3cdk110n9cx6rzpgrxjz4dl6sghqpjj4hvh37axv7f8p52f02")))) (properties `((upstream-name . "Rdisop"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/sneumann/Rdisop") (synopsis "Decomposition of isotopic patterns") (description @@ -8738,14 +9913,14 @@ be calculated to search in MS peak lists.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "3.0.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0497b43wxcfqyr4k30f0xq7yillb4fz0gqiqxxp66gvnqv4wiv6v")))) + "099j1hmmqqs6v5gffxxvizv784ildadqg6kicfshb45ykc8kkvzm")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -8767,15 +9942,38 @@ of other R packages who wish to make use of HTSlib.") (define-public r-rnbeads (package (name "r-rnbeads") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RnBeads" version)) (sha256 - (base32 "0v7dzmbyskq0vmja09dncg1g50dl3iycg883swb7lfvi4xzr42vj")))) - (properties `((upstream-name . "RnBeads"))) + (base32 "006kmfg1lysa9z9cbc507l54xh1apslrxxk41w65zp7bqkhs2zj9")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "inst/bin")))) + (properties + `((upstream-name . "RnBeads") + (updater-extra-inputs . ("kentutils")) + (updater-extra-native-inputs + . ("r-impute" "r-missmethyl" "r-doparallel" "r-qvalue" "ghostscript")))) (build-system r-build-system) + (arguments + (list + ;; Vignette ‘RnBeads.Rnw’ overwrites the following ‘tangle’ output by + ;; vignette ‘RnBeads_Annotations.Rnw’: RnBeads_Annotations.R + #:test-types '(list "tests") + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'link-to-executables + (lambda* (#:key inputs #:allow-other-keys) + (let ((bin (string-append #$output + "/site-library/RnBeads/bin/linux_x86.64"))) + (mkdir-p bin) + (symlink (search-input-file inputs "/bin/bedToBigBed") + (string-append bin "/bedToBigBed")) + (symlink (search-input-file inputs "/bin/bedGraphToBigWig") + (string-append bin "/bedGraphToBigWig")))))))) (propagated-inputs (list r-biocgenerics r-cluster @@ -8793,23 +9991,56 @@ of other R packages who wish to make use of HTSlib.") r-methylumi r-plyr r-s4vectors)) + (inputs (list kentutils)) + (native-inputs + (list ghostscript + r-doparallel + r-impute + r-missmethyl + r-qvalue + r-rnbeads-hg19 + r-rtracklayer + r-runit)) (home-page "https://bioconductor.org/packages/RnBeads") (synopsis "RnBeads") (description - "@code{RnBeads} facilitates comprehensive analysis of various types of DNA -methylation data at the genome scale.") + "@code{RnBeads} facilitates comprehensive analysis of various types of +DNA methylation data at the genome scale.") (license license:gpl3))) +(define-public r-rpx + (package + (name "r-rpx") + (version "2.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rpx" version)) + (sha256 + (base32 "0w2nxcd2v8rc3spi0rb96d3r7hp2dh7f7k50n0mik626fy1i0yc5")))) + (properties `((upstream-name . "rpx"))) + (build-system r-build-system) + ;; Tests require Internet access. + (arguments (list #:tests? #false)) + (propagated-inputs (list r-biocfilecache r-curl r-jsonlite r-rcurl r-xml2)) + (native-inputs (list r-biostrings r-knitr r-testthat r-tibble)) + (home-page "https://github.com/lgatto/rpx") + (synopsis "R interface to the ProteomeXchange Repository") + (description + "The rpx package implements an interface to proteomics data submitted to +the @code{ProteomeXchange} consortium.") + (license license:gpl2))) + (define-public r-impute (package (name "r-impute") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "1g0m9298srkhjnq3mc5rd7krr9y3cy74yvg9k0j7ypc9nmgcqabr")))) + "19w88r5c9c522jafl4bdxravphpxady3n8bkd17vngxvla9m257z")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -8823,13 +10054,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplay (package (name "r-interactivedisplay") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplay" version)) (sha256 (base32 - "14k1j8bmpbrldx61fbvn20f7l2lc50bj9iy01a5jf0ddcbi27x5g")) + "1gqn93j7ysa34qgwv1166a51n817zm1pcghx7i7wjaiazbs9rlv9")) (snippet '(for-each delete-file '("inst/www/js/d3.v2.js" @@ -8888,6 +10119,8 @@ microarray data, using nearest neighbor averaging.") (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) + ("r-runit" ,r-runit) + ;; D3 version 2.10.3 ("js-d3-v2" ,(origin (method url-fetch) @@ -8895,7 +10128,9 @@ microarray data, using nearest neighbor averaging.") (sha256 (base32 "1m57mxhcynfaz6gz3v0aph5i6hx5jf455jdygyl8yzs9r2dpp5vr")))) + ;; Version 1.9.4 is bundled ("js-datatables-1.9" ,js-datatables-1.9) + ;; Version 1.10.0 is bundled ("js-datatables-1.10" ,js-datatables) ("js-jquery-1.8.2" ,(origin @@ -8922,14 +10157,14 @@ visualizations and interfaces for working with Bioconductor data.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0ih9b6n81gr84vhmwcq49knrbmkwbh50gy5hrap654nicb3j3jzb")))) + "1w39vn00armnka9sbgczc0madwc3hmcn4awcyl1xbq86q8danx11")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -8947,16 +10182,18 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "09qdsdbz5ha3b2fafwv80n6pdajjgsc5w52n1dy6ds41vxgf0jis")))) + "19jy6nl46krlspzyqgmyix0d53izrdy3yx69nlamzph4gwjf5m0f")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) + ;; Tests contact the internet. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biostrings r-httr r-png)) (native-inputs @@ -8971,13 +10208,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lea (package (name "r-lea") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "LEA" version)) (sha256 (base32 - "0r6nj6ck77fhbmqifbx4srj1f3yr7haiinphcm0p4g8b7zn4a6fm")))) + "0ayc6gqw426ygdj6fsixqfyq8br3szz3ghmn85rq4bizdabnkjpg")))) (properties `((upstream-name . "LEA"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -9002,17 +10239,17 @@ scale with the dimensions of large data sets.") (define-public r-lfa (package (name "r-lfa") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "1sbgr6h2kpfpzw3fkqd1075wrmbblb97pdywmvl8xv52vg0wqxz3")))) + (base32 "00lrspaayb03dq7j786ph52s1yp6chdzcvz9b62izycsvsfpy8z1")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor r-rspectra)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/StoreyLab/lfa") (synopsis "Logistic Factor Analysis for categorical data") (description @@ -9023,15 +10260,15 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.60.4") + (version "3.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "123z062fc0qf43zplmw5svzpdmpgxagyl1gi1bxa34426s1hfv6m")))) + "02744ahl5nbmj5gif20vyqqra2fldv3dskg2m6r1yqi830s0957f")))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-go-db r-knitr r-locfit r-mass r-org-hs-eg-db)) (propagated-inputs (list r-statmod)) (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -9077,7 +10314,7 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") r-robustbase r-tibble r-vegan)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "http://huttenhower.sph.harvard.edu/maaslin2") (synopsis "Multivariable association discovery in population-scale meta-omics studies") @@ -9092,13 +10329,13 @@ of data exploration, normalization, and transformation methods.") (define-public r-made4 (package (name "r-made4") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "0x96lhkz0fwp3qis8k2lllmi520b887bz26jcq3zlk1kjhbg91a8")))) + "0z40f2bxnakplq3xx221fk51m830dixc7nfll4xw1r3g2pg1iraq")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs @@ -9121,13 +10358,13 @@ datasets (coinertia analysis).") (define-public r-makecdfenv (package (name "r-makecdfenv") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "makecdfenv" version)) (sha256 (base32 - "0c1ks5f2rc0mwbfji6iicvypbmm46mq8yckmdpwiyp22l7l05aqz")))) + "08d33iqbgczw4w63s5nrjzwy059mqzgcr9s1g59irgplr9szjiar")))) (properties `((upstream-name . "makecdfenv"))) (build-system r-build-system) (inputs (list zlib)) @@ -9148,13 +10385,13 @@ package that automatically loads that environment.") (define-public r-manor (package (name "r-manor") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MANOR" version)) (sha256 - (base32 "0mlhv4gy4bxvdm0drwwrm4x48wy0mghzcqhvaw2rhw0h65rmy5ps")))) + (base32 "0v99f4pkjgz5qjj68xsabfh5prgkz0fjlqn8yn7f1d4sv8cigq6l")))) (properties `((upstream-name . "MANOR"))) (build-system r-build-system) (propagated-inputs (list r-glad)) @@ -9171,13 +10408,13 @@ experiments.") (define-public r-maser (package (name "r-maser") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maser" version)) (sha256 (base32 - "0w62dl65ysgcwixgmmb70qp6f85vhfnqjsww5snkjd48ypwx65ca")))) + "0vpi1qdkscnxxbfx3py8szw9429wc4vkwls9b4w1zq1zrvvzbaig")))) (properties `((upstream-name . "maser"))) (build-system r-build-system) (propagated-inputs @@ -9192,7 +10429,7 @@ experiments.") r-iranges r-reshape2 r-rtracklayer)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/DiogoVeiga/maser") (synopsis "Mapping alternative splicing events to proteins") (description @@ -9203,13 +10440,13 @@ and visualizaton of alternative splicing events generated by rMATS.") (define-public r-mdqc (package (name "r-mdqc") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mdqc" version)) (sha256 - (base32 "1frn6s43j6sbwnb5h2hykccvi7cwbasp8l37rc3nkxpc6szvsby6")))) + (base32 "0vxplgmfhp0g8v080h0rwvkzhq3gq1956p4jngkrz4nmpynzdfd7")))) (properties `((upstream-name . "mdqc"))) (build-system r-build-system) (propagated-inputs @@ -9228,17 +10465,17 @@ high distances can be flagged as potentially low-quality.") (define-public r-metabocoreutils (package (name "r-metabocoreutils") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaboCoreUtils" version)) (sha256 - (base32 "1y5lq1x60pcvxsl8dim5plzd3y4bqjkcam5hv9614xw0sr4h0r04")))) + (base32 "0gwghyc59cjp9arrwzm9j643a1nkl14mmcmadw55x7i9gyxvdils")))) (properties `((upstream-name . "MetaboCoreUtils"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-mscoreutils)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/RforMassSpectrometry/MetaboCoreUtils") (synopsis "Core utils for Metabolomics data") (description @@ -9263,6 +10500,14 @@ mixes commonly used in MS experiments.") (base32 "0bjbiwbgs0lv0j6gjv5rhqhmqk0p7f80lfig4n24i4bqwkd2j26k")))) (properties `((upstream-name . "metagenomeSeq"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Two tests fail with accuracy problems. + (delete-file "tests/testthat/test-fitZig.R")))))) (propagated-inputs (list r-biobase r-foreach @@ -9273,7 +10518,7 @@ mixes commonly used in MS experiments.") r-matrixstats r-rcolorbrewer r-wrench)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/HCBravoLab/metagenomeSeq") (synopsis "Statistical analysis for sparse high-throughput sequencing") (description @@ -9288,13 +10533,13 @@ correlations.") (define-public r-metaneighbor (package (name "r-metaneighbor") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaNeighbor" version)) (sha256 (base32 - "0sz15njb0y9vcmbv89k3x2sw4px8nmy3qhqkvyl69kxlcqdicgxi")))) + "1pmnxkf893zhvxyyihc10xfn18y742v82mxj538r6q3x08wp9gj8")))) (properties `((upstream-name . "MetaNeighbor"))) (build-system r-build-system) (propagated-inputs @@ -9310,7 +10555,7 @@ correlations.") r-summarizedexperiment r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/MetaNeighbor") (synopsis "Single cell replicability analysis") (description @@ -9324,14 +10569,16 @@ profiles than cells of different types.") (define-public r-methylaid (package (name "r-methylaid") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MethylAid" version)) (sha256 - (base32 "084mnllaj6qp5ai5bmj6wgc90bs270qbzl60sch1f863x8fv9lzr")))) - (properties `((upstream-name . "MethylAid"))) + (base32 "0iq4ba4hsf7zwb063gqf00al031lydpg0yhlxwx8aczmyly00a9q")))) + (properties + `((upstream-name . "MethylAid") + (updater-ignored-native-inputs . ("r-methylaiddata")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -9345,7 +10592,11 @@ profiles than cells of different types.") r-rcolorbrewer r-shiny r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-geoquery + r-knitr + r-minfidata + r-minfidataepic + r-runit)) (home-page "https://git.bioconductor.org/packages/MethylAid") (synopsis "Quality control of large Illumina DNA Methylation array data sets") @@ -9362,13 +10613,13 @@ be explored.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "000dvi63cjikjbq3q83hlspd7y62rpswzg6hs5z1z1pj6a8rifdj")))) + "1niblg067819p8mldnlkf7xd8g3k89q6wcj095idlkcna06xj3d1")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9392,7 +10643,7 @@ be explored.") r-s4vectors r-zlibbioc)) (native-inputs - (list r-knitr)) ; for vignettes + (list r-knitr r-testthat)) ; for vignettes (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") @@ -9409,13 +10660,13 @@ TAB-Seq.") (define-public r-mfuzz (package (name "r-mfuzz") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Mfuzz" version)) (sha256 (base32 - "00sx63bg5qw22vw0yw3syhyl5ffjrqvf81b9ksgw2p0z3yiiss5h")))) + "1217hd20byymrldzydp3r9qmvssznzy1yggdsdm1hbcvrvrxmd4s")))) (properties `((upstream-name . "Mfuzz"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-tkwidgets)) @@ -9480,7 +10731,7 @@ time-series data (including a graphical user interface).") r-metafor r-stringr r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/MMUPHin") (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome") (description @@ -9497,13 +10748,13 @@ It has function interfaces for: (define-public r-modstrings (package (name "r-modstrings") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Modstrings" version)) (sha256 - (base32 "0yc8gsgxlww2g9z1m6jl02aqmama10fkr2mvibvdi01s5pqwdbky")))) + (base32 "1jffh3ril1lwggfva8k319mang0i75xrk6fkp0xk6kp1979qpyxz")))) (properties `((upstream-name . "Modstrings"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -9515,7 +10766,7 @@ It has function interfaces for: r-stringi r-stringr r-xvector)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/Modstrings") (synopsis "Working with modified nucleotide sequences") (description @@ -9531,6 +10782,49 @@ are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.") (license license:artistic2.0))) +(define-public r-mosdef + (package + (name "r-mosdef") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mosdef" version)) + (sha256 + (base32 "0y2hniyb1y5hxlsm339059kb4n3l21fzb3xx112igsbk7zd0r258")))) + (properties + `((upstream-name . "mosdef") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-pcaexplorer")))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-clusterprofiler + r-deseq2 + r-dt + r-ggforce + r-ggplot2 + r-ggrepel + r-go-db + r-goseq + r-htmltools + r-rcolorbrewer + r-rlang + r-s4vectors + r-scales + r-summarizedexperiment + r-topgo)) + (native-inputs (list r-knitr r-macrophage r-org-hs-eg-db r-testthat)) + (home-page "https://github.com/imbeimainz/mosdef") + (synopsis "Frequently used and useful differential expression functions") + (description + "This package provides functionality to run a number of tasks in the +differential expression analysis workflow. This encompasses the most widely +used steps, from running various enrichment analysis tools with a unified +interface to creating plots and beautifying table components linking to +external websites and databases. This streamlines the generation of +comprehensive analysis reports.") + (license license:expat))) + (define-public r-motifrg (package (name "r-motifrg") @@ -9561,14 +10855,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "1gafcq3p693f28gz3p8hk8mlxd9zja95h8953sr56n7krfffy1gi")))) + "04kni9lv04dsnam71dw3ib2jmjfrrndj9432igf5aj22l4wlxbc3")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -9588,6 +10882,7 @@ throughput genetic sequencing data sets using regression methods.") r-matrixstats r-progress r-purrr + r-rlang r-s4vectors r-scales r-scater @@ -9597,7 +10892,7 @@ throughput genetic sequencing data sets using regression methods.") r-summarizedexperiment r-variancepartition r-viridis)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/HelenaLC/muscat") (synopsis "Multi-sample multi-group scRNA-seq data analysis tools") (description @@ -9611,24 +10906,21 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0smf4l023ckwsm5ckrqqw7kjyi1awp378mzhab7v8nk9n5smsj61")))) + "16a5g9l025pj7xrl3g78nkqyrcnldj8y2025ibvsfg0921zyqiyp")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-ccfindr r-knitr r-testthat)) (propagated-inputs (list r-biocgenerics r-biostrings r-bsgenome - ;; These two packages are suggested packages - r-bsgenome-hsapiens-1000genomes-hs37d5 - r-bsgenome-hsapiens-ucsc-hg19 r-cowplot r-dplyr r-genomeinfodb @@ -9646,7 +10938,11 @@ platform that mimics both single and multi-sample scRNA-seq data.") r-stringr r-tibble r-tidyr - r-variantannotation)) + r-variantannotation + + ;; These two packages are suggested packages + r-bsgenome-hsapiens-ucsc-hg19 + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") (description "This package provides an extensive toolset for the @@ -9657,13 +10953,13 @@ in SNV base substitution data.") (define-public r-msa (package (name "r-msa") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msa" version)) (sha256 (base32 - "16ixhinhcbf2nvdmqria231s4qhr8lzhr7yqr7ljrnnwiqadfr67")))) + "0v65pfhl19zi0dc2avzpxq7dygknlr2y44wkir6wmvn8m7jppjlg")))) (properties `((upstream-name . "msa"))) (build-system r-build-system) (propagated-inputs @@ -9685,19 +10981,84 @@ function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.") (license license:gpl2+))) +(define-public r-msbackendsql + (package + (name "r-msbackendsql") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MsBackendSql" version)) + (sha256 + (base32 "0hs4nh3bij5jzscdjjfkq2agcpysyy7ziv40713z7p7ai6wkppyj")))) + (properties `((upstream-name . "MsBackendSql"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-biocparallel + r-data-table + r-dbi + r-iranges + r-mscoreutils + r-progress + r-protgenerics + r-s4vectors + r-spectra)) + (native-inputs (list r-knitr r-msdata r-mzr r-rsqlite r-testthat)) + (home-page "https://github.com/RforMassSpectrometry/MsBackendSql") + (synopsis "SQL-based mass spectrometry data backend") + (description + "This package provides an SQL-based mass spectrometry (MS) data backend +supporting also storage and handling of very large data sets. Objects from +this package are supposed to be used with the Spectra Bioconductor package. +Through the @code{MsBackendSql} with its minimal memory footprint, this +package thus provides an alternative MS data representation for very large or +remote MS data sets.") + (license license:artistic2.0))) + (define-public r-msnbase (package (name "r-msnbase") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0cdvi2mjvhj0h8x2rh3kkzrdnmzhr7d9a41m21r6b843a0q7hp6f")))) - (properties `((upstream-name . "MSnbase"))) + "0cykb5kk524i3ssps798c7wfpa3f8svdgxa8sfvc1pxm0fxypfgb")))) + (properties + `((upstream-name . "MSnbase") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-prolocdata")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Needs r-prolocdata + (for-each delete-file + '("tests/testthat/test_average.R" + "tests/testthat/test_fdata-selection.R" + "tests/testthat/test_foi.R" + "tests/testthat/test_nadata.R" + "tests/testthat/test_trimws.R" + "tests/testthat/test_MSnSet.R")) + ;; Attempts to run "hostname" + (delete-file "tests/testthat/test_readMSData2.R") + ;; Needs Internet access + (for-each delete-file + '("tests/testthat/test_fileNames.R" + "tests/testthat/test_MSmap.R" + "tests/testthat/test_MzTab.R" + "tests/testthat/test_MzTab_09.R")) + ;; Fails with: object 'hyperLOPIT2015' not found + (delete-file "tests/testthat/test_utils.R") + ;; Fails with: invalid 'description' argument + (delete-file "tests/testthat/test_io.R")))))) (propagated-inputs (list r-affy r-biobase @@ -9722,7 +11083,12 @@ package TeXshade.") r-scales r-vsn)) (native-inputs - (list r-knitr)) + (list r-knitr + r-msdata + r-rpx + r-summarizedexperiment + r-testthat + r-xml)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -9733,19 +11099,23 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0misrm4x4z5h8dfwcrwi24nhcjslqvbyk5n7qz6kf2zcgcwq8q44")))) + "1mdd7k71w8iiy9wkdaaq78y23547i7rcx5zn2rqzh09rgz68dnni")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; Disable vignettes because they need Internet access. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases + ;; Needed for r-r-cache (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs @@ -9775,6 +11145,7 @@ of mass spectrometry based proteomics data.") r-stringr r-tibble r-xtable)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description @@ -9790,14 +11161,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0kh9swzh3hvi6qi64cgr13f22s1mgvz2rid5psb1gy4l3biwadj5")))) + "0lf7w65v01mc7cawlsbjagbrhlh6jpy6ah7pbjgyvy5s0axlzgp2")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9808,7 +11179,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") r-protgenerics r-xml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -9821,14 +11192,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "02dz23xns9ryz98nip1w68h9q5ckxpyl1zvzklsp4j7p9z2400dk")) + "1vqd9arlhvhw58jk2r343x6dqbv85ckgzjk04hi3pb6w5z0yvks4")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) @@ -9859,7 +11230,7 @@ specific parser.") r-rcpp r-rhdf5lib)) (native-inputs - (list r-knitr)) + (list r-codetools r-knitr r-msdata r-mzid r-runit r-xml)) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -9917,6 +11288,7 @@ previously been used in XCMS.") r-tidyr r-vcfr r-zoo)) + (native-inputs (list r-testthat)) (home-page "https://github.com/kharchenkolab/numbat") (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") (description @@ -9941,14 +11313,14 @@ Gao et al in Nature Biotechnology 2022}.") (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "03z5pyqbaxwyrq5m858c8k69fwvclq98ksr84dc4m7r8lzz2hfxx")))) + "0phm4vl879ak98rjffb7z3khwrsmjd814y86zidmfailwrzmp3xx")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs @@ -9966,7 +11338,11 @@ Gao et al in Nature Biotechnology 2022}.") r-rsqlite r-s4vectors r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-knitr + r-testthat + r-txdb-hsapiens-ucsc-hg38-knowngene + r-txdb-mmusculus-ucsc-mm10-ensgene)) (home-page "https://bioconductor.org/packages/Organism.dplyr") (synopsis "Dplyr-based access to Bioconductor annotation resources") (description @@ -9980,16 +11356,18 @@ functionality of the @code{TxDb} packages (e.g., (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "1cfh632rpmklmyd5cibwiy0i2pk2kk2m39g8mq5sxfwd2am4r0jk")))) + "1xbwvpxcn23yvibsf12g9irxcmz6ckp87991zzmk449xckayavrx")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) + ;; Tests need r-homo-sapiens, which needs this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-biobase @@ -10003,7 +11381,7 @@ functionality of the @code{TxDb} packages (e.g., r-rbgl r-s4vectors r-txdbmaker)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several @@ -10014,16 +11392,17 @@ the fact that each of these packages implements a select methods.") (define-public r-oscope (package (name "r-oscope") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Oscope" version)) (sha256 (base32 - "16d2ngakdg73rdx0bf1pz3z1n8npjzl3b7dn94g9zbayw4vp3x5z")))) + "02ysp86ssx1w9vmm4yc674xlhnclksh3f25skb8c9z4axi5708hk")))) (properties `((upstream-name . "Oscope"))) (build-system r-build-system) - (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq)) + (native-inputs (list r-testthat)) (home-page "https://bioconductor.org/packages/Oscope") (synopsis "Oscillatory genes identifier in unsynchronized single cell RNA-seq") @@ -10040,14 +11419,14 @@ insertion module to recover the base cycle order for each oscillator group.") (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.30.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "1szl2gyhw55ad4phcb7qn14amjb6xg65l3p4hnjzp6rda2cy9437")))) + "1i5qzbwdgi59izgppz63mvddiph7qv48h75243capxqfhbcqkq1g")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs @@ -10066,6 +11445,7 @@ insertion module to recover the base cycle order for each oscillator group.") r-iranges r-knitr r-limma + r-mosdef r-nmf r-pheatmap r-plotly @@ -10081,7 +11461,7 @@ insertion module to recover the base cycle order for each oscillator group.") r-threejs r-tidyr r-topgo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-airway r-knitr r-org-hs-eg-db r-testthat)) (home-page "https://github.com/federicomarini/pcaExplorer") (synopsis "Interactive Visualization of RNA-seq Data Using a Principal Components Approach") @@ -10095,14 +11475,14 @@ application encapsulates the whole analysis.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.96.0") + (version "1.98.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1hrq0xmpr1l95hyi6ls9r86ahwf2rcbvr8m7cpg6ra0gsfyn4mpi")))) + "02p9ax76wm4rfkz9hmrf95xvq91ckha689qkg6lpwgb8f81wga7j")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -10122,13 +11502,13 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-pfamanalyzer (package (name "r-pfamanalyzer") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pfamAnalyzeR" version)) (sha256 (base32 - "06bp5nghgrj8qyzqp1v869vck1j10093r9dp67w0kav4x4srkyyl")))) + "1d14nhi4gndg8gr4fk4yvfnjcvin9rndram0xhnjrkia166p1msx")))) (properties `((upstream-name . "pfamAnalyzeR"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble)) @@ -10145,13 +11525,13 @@ domain isotypes from pfam data.") (define-public r-piano (package (name "r-piano") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "piano" version)) (sha256 - (base32 "0v168wkwxzh70h2c08ad4dzlgklbgvx1fzwrzw2mqq0fyczj0diw")))) + (base32 "037xgsb57gc1ysb0p1nsb9mhfv7lgry3anza0znyhb3wbnjzz1q4")))) (properties `((upstream-name . "piano"))) (build-system r-build-system) (propagated-inputs @@ -10210,13 +11590,13 @@ comparisons of methods for differential expression.") (define-public r-powertcr (package (name "r-powertcr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "powerTCR" version)) (sha256 - (base32 "04w6jhpc1vkqrm3dr5igp1iwkammmi53mqafjz694n379hamxrhg")))) + (base32 "0xkqzh0bkji5acca3xcc68xqryyxvizgka5nabbw5w14zhrnymx5")))) (properties `((upstream-name . "powerTCR"))) (build-system r-build-system) (propagated-inputs @@ -10229,7 +11609,7 @@ comparisons of methods for differential expression.") r-truncdist r-vegan r-vgam)) - (native-inputs (list r-knitr)) + (native-inputs (list r-biocgenerics r-knitr r-runit)) (home-page "https://bioconductor.org/packages/powerTCR") (synopsis "Model-based comparative analysis of the TCR repertoire") (description @@ -10283,13 +11663,13 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (define-public r-psmatch (package (name "r-psmatch") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PSMatch" version)) (sha256 - (base32 "13w145is3d95392qqdq6qh3mrlcixbj0jzz4r590xas1qjp5d03h")))) + (base32 "1aq6kdvw5n0d9c8pg7clfbpm5v52svx438sk5wphj4x0l3qvbdhh")))) (properties `((upstream-name . "PSMatch"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -10300,7 +11680,7 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") r-protgenerics r-qfeatures r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-msdata r-mzid r-mzr r-spectra r-testthat)) (home-page "https://github.com/RforMassSpectrometry/PSM") (synopsis "Handling and managing peptide spectrum matches") (description @@ -10315,13 +11695,13 @@ fragment ions.") (define-public r-protgear (package (name "r-protgear") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "protGear" version)) (sha256 - (base32 "1wbdp7f55lbn0gcxgnp9xk0y5npn7jmk9vp7yq9v76j7f396vj2f")))) + (base32 "0nhx40i7mh5y0yd2crlshxq0844yfvjakpdgd86w9y3c7879bs69")))) (properties `((upstream-name . "protGear"))) (build-system r-build-system) (arguments @@ -10377,16 +11757,17 @@ batch correction and normalization.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "0h0i4dgsgvyhma5pfvycv6wyxv27vp0b2i8b6l8hj55z8cvmvfln")))) + "0pg7rqz0ixaiihqybynm94qvdc5y953xzxzxvwv5gbmxdk9s3lmk")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/lgatto/ProtGenerics") (synopsis "S4 generic functions for proteomics infrastructure") (description @@ -10397,17 +11778,18 @@ proteomics packages.") (define-public r-pwalign (package (name "r-pwalign") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pwalign" version)) (sha256 - (base32 "1m0j1m5jif5spd9fkpzz3z3c9s8vwiy8xvpx8rz8igxj89rwrwb7")))) + (base32 "1i01xhg8sjz9gx5pqaq8wam9r13l8m9n9pf1aiavjif20gd0rz3b")))) (properties `((upstream-name . "pwalign"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biostrings r-iranges r-s4vectors r-xvector)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/pwalign") (synopsis "Perform pairwise sequence alignments") (description @@ -10421,19 +11803,19 @@ matrix for a set of strings.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "1n6rfrcvlgi6mzz36v9sniqr05xfjzvfdpv4xwsn1xq41326wdv3")))) + "04sy7kgsjvwlzr6r3lnyrk6l7d9jqfqqzlfcs0b90ciq8gldxlw8")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs (list r-bh r-graph)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description @@ -10444,15 +11826,31 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0ll0sj2zyazw0nxbpybq9frmxvmcjkgk3hwp3flnysjxg056dhxg")))) + "0sg3ngb7jwh8gyhmmm7fkxn9ixj590j47rfcfdcnbbk9pwd9y07p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'unpack 'skip-bad-tests + (lambda _ + ;; These tests need Internet access. + (with-directory-excursion "tests/testthat" + (substitute* "test_database_functions.R" + ((".*Testing createDB function.*" m) + (string-append m "skip('guix')\n"))) + (delete-file "test_report.R") + (delete-file "test_motif.R"))))))) + (inputs (list pandoc)) (propagated-inputs (list r-biocgenerics r-biostrings @@ -10482,7 +11880,7 @@ the graph algorithms contained in the Boost library.") r-seqlogo r-txdbmaker)) (native-inputs - (list r-knitr)) + (list r-biocmanager r-knitr r-testthat)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -10494,13 +11892,13 @@ library implementing most of the pipeline's features.") (define-public r-rcy3 (package (name "r-rcy3") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCy3" version)) (sha256 - (base32 "03zmskcb8n87x6m5jlhsh2b0b2qjk91y16fdcj3kz5c1j7zfs18i")))) + (base32 "17bclz2bv7xzzx2rgpd89d19vlkkv0i67vcrva0v0gxm1cf4zvs1")))) (properties `((upstream-name . "RCy3"))) (build-system r-build-system) (propagated-inputs (list r-base64enc @@ -10531,16 +11929,26 @@ with a single RCy3 function.") (define-public r-regioner (package (name "r-regioner") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "1ygdlqvhf165mqd247783pi1yzidqap8b913444vrs881n62xvrb")))) + "1226wljfndqs11p61a79b0rm66jzwljzzi8w9lhx9g165jy3xxay")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests require internet access. + (for-each delete-file + '("tests/testthat/test_randomizationFunctions.R" + "tests/testthat/test_toGRanges.R"))))))) (propagated-inputs (list r-biostrings r-bsgenome @@ -10551,7 +11959,7 @@ with a single RCy3 function.") r-rtracklayer r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-biocmanager r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -10562,18 +11970,21 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0vq46dj2v3imjmf6cw8mab6k9v4rrc5r2vh100jjlsm3z15gvl17")) + "1w749cn04lkicdb5p9xw4zs2i7i6810m8wm10lpvcby66lja1d7l")) (snippet '(delete-file "inst/extdata/jslib/jquery-1.8.0.min.js")))) (properties - `((upstream-name . "ReportingTools"))) + `((upstream-name . "ReportingTools") + ;; This is mentioned in microarrayAnalysis.Rnw, but the package doesn't + ;; exist and apparently isn't needed after all. + (updater-ignored-native-inputs . ("r-gsealm")))) (build-system r-build-system) (arguments (list @@ -10614,7 +12025,17 @@ region sets and other genomic features.") r-r-utils r-xml)) (native-inputs - (list esbuild r-rmarkdown + (list esbuild + r-all + r-genefilter + r-hgu95av2-db + r-org-hs-eg-db + r-org-mm-eg-db + r-org-sc-sgd-db + r-pasilla + r-rmarkdown + r-runit + r-shiny (origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.8.0.js") @@ -10638,18 +12059,29 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "086bnwzmlwq3z9a4kb1rnzb2wnchhi4gvzpijhladgd83nqyb0wn")))) + "0qjz5592ziy1f0dskdn2xvi0jm7wxpnjgvjcvwmp3jgzs2s84p3b")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Some of the tests expect to be able to use the proprietary + ;; SZIP, which we've removed from r-rhdf5lib. + (for-each delete-file + '("tests/testthat/test_H5P_dcpl.R" + "tests/testthat/test_h5read.R"))))))) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) (native-inputs - (list r-knitr)) + (list r-bit64 r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -10665,14 +12097,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "0fsfp34pfb5k030j7nfx9b9vsil02y85sv1dd1y0bfdxchi4bw8x")))) + "1kf8w5bq20gwmry2dj46zhnbidpf94ldwpaix3arr4mjkxb7s9va")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (arguments @@ -10695,13 +12127,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "04lz0dzwmgi8j9wyspbmjln6yb5fv4f538nqyrfd31d0g16937b8")))) + "0wqh1spqmf30cv3v0v5bawpjwfjrlnxz2n8cc0a11c2kbbdxrnr5")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -10726,7 +12158,7 @@ HDF5 datasets.") r-s4vectors r-xvector r-zlibbioc)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") (synopsis "Interface to samtools, bcftools, and tabix") (description @@ -10753,6 +12185,7 @@ tab-delimited (tabix) files.") (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description @@ -10762,15 +12195,17 @@ tab-delimited (tabix) files.") (define-public r-rtcga (package (name "r-rtcga") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGA" version)) (sha256 (base32 - "1a967id4anjzpdlbdd8a85fvb1z7mcr759pr91aashv12bzzhnk0")))) + "0x6fxfc75gkkvmp9ah7v0c0kg8v9m6jnysygvj76r62bkqziigr4")))) (properties `((upstream-name . "RTCGA"))) (build-system r-build-system) + ;; Tests need r-rtcga-rnaseq, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-assertthat r-data-table r-dplyr @@ -10789,7 +12224,7 @@ tab-delimited (tabix) files.") r-viridis r-xml r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://rtcga.github.io/RTCGA/") (synopsis "The Cancer Genome Atlas data integration") (description @@ -10807,13 +12242,13 @@ transforms TCGA data to tidy form which is convenient to use.") (define-public r-rtcgatoolbox (package (name "r-rtcgatoolbox") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGAToolbox" version)) (sha256 (base32 - "0l4idk6gsrnm7laj1xkm6jwmyy5l90kphm21zk7y33cpnp2ryjwr")))) + "1824p551155qj7g85wb2spp6v77hjl37s86zy9n2zyfkwiwg321y")))) (properties `((upstream-name . "RTCGAToolbox"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -10846,17 +12281,20 @@ pre-processed data.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0h2cqr1jqqqxvkmqpngfl8ppm1p65vvlb1wgfwl9r4f99b8vz33g")))) + "0gh91rxahdh3ablngm094mnyrdrklm70cjlhwjwz2rydbr3a6dbg")))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; Tests require internet access. + #:tests? #false + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'use-system-zlib (lambda _ (substitute* "DESCRIPTION" @@ -10866,7 +12304,7 @@ pre-processed data.") (native-inputs (list pkg-config)) (inputs - (list curl openssl zlib)) + (list openssl zlib)) (propagated-inputs (list r-biocgenerics r-biocio @@ -10926,13 +12364,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-saturn (package (name "r-saturn") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "satuRn" version)) (sha256 (base32 - "03mlb4j219w8760zm5hnryjwxns3qz9y3wl6zaqdfnl94bwyl9r8")))) + "0rfh0zprl1gibcanjwp4sncjv5k660lhylbiaqwgri7n62jz7k9m")))) (properties `((upstream-name . "satuRn"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -10943,7 +12381,7 @@ differential expression analysis, RNAseq data and related problems.") r-matrix r-pbapply r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/statOmics/satuRn") (synopsis "Analysis of differential transcript usage for scRNA-seq applications") @@ -10960,13 +12398,13 @@ transcripts in groups of interest.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "1gzssp7im1d9pp2mbar27k854fcc3rqyza5d77flmhshq88xrskv")))) + (base32 "0gra749fgcify2625gg1nbnqw328ddf98pplv8yaq4hn37a1s76j")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs @@ -10983,7 +12421,7 @@ transcripts in groups of interest.") r-seurat r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/grisslab/scAnnotatR") (synopsis "Pretrained models for prediction on single cell RNA-sequencing data") (description @@ -10997,13 +12435,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "1np3arhjxxgif68i0wi0nqqbrwavy14dh9vy2g9mw4408k7789w0")))) + (base32 "0cfv1bi0vm217bhwqplp89i6j10di41pg1k22qp1n9q6ah41wada")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -11028,7 +12466,7 @@ cell types based on specific research needs.") r-singlecellexperiment r-summarizedexperiment r-xgboost)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/plger/scDblFinder") (synopsis "Detect multiplets in single-cell RNA sequencing data") (description @@ -11110,6 +12548,7 @@ with respect to the cell population of interest.") r-rhpcblasctl r-stringr r-tidygraph)) + (native-inputs (list r-testthat)) (home-page "https://github.com/kharchenkolab/scistreer") (synopsis "Maximum-likelihood perfect phylogeny Inference at scale") (description @@ -11122,13 +12561,13 @@ method applicable to massive single-cell datasets (>10,000 cells).") (define-public r-scmap (package (name "r-scmap") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "0acy3sg4j36znsfxpkb190wbawbngx15cr5x2lhgrjivvw3637x1")))) + (base32 "16ajd19p8ybllm80sr7p6zv8jxs8y4r9cblgzy9f12bby2l71fbz")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -11164,17 +12603,18 @@ different experiment.") (define-public r-screpertoire (package (name "r-screpertoire") - (version "2.0.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scRepertoire" version)) (sha256 - (base32 "1ifnyfzswisacvxxf041l1snfv1b8x30pjg2pwampg804c56f1wj")))) + (base32 "0id62pkjyk48jxica8mfzb2mzwc5f1ijb7d5200grxzn453zsihm")))) (properties `((upstream-name . "scRepertoire"))) (build-system r-build-system) (propagated-inputs - (list r-cubature + (list r-assertthat + r-cubature r-dplyr r-evmix r-ggalluvial @@ -11184,7 +12624,9 @@ different experiment.") r-hash r-igraph r-inext + r-lifecycle r-plyr + r-purrr r-quantreg r-rcpp r-reshape2 @@ -11199,7 +12641,7 @@ different experiment.") r-tidygraph r-truncdist r-vgam)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/scRepertoire") (synopsis "Toolkit for single-cell immune receptor profiling") (description @@ -11215,14 +12657,14 @@ powerTCR R packages.") (define-public r-scrnaseq (package (name "r-scrnaseq") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scRNAseq" version 'experiment)) (sha256 - (base32 "0jsq037ba4xsb3bwwf021jw2hqv30vb5nrjag97xadx75z5fzqlr")))) + (base32 "1vjww44d3w2rvvj1b2fdbcv0pwpsspqdhzbykwvsqmw559k9viz1")))) (properties `((upstream-name . "scRNAseq"))) (build-system r-build-system) (propagated-inputs (list r-alabaster-base @@ -11245,7 +12687,7 @@ powerTCR R packages.") r-singlecellexperiment r-sparsearray r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/scRNAseq") (synopsis "Collection of public single-cell RNA-seq datasets") (description @@ -11257,13 +12699,13 @@ with cell- and gene-level metadata.") (define-public r-scry (package (name "r-scry") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "16489ff1nc798nfcmqvqaczm7hqffkhpad1dfgr7dxlahd8sbnw9")))) + "09l8w1b2n8kwhmn8373hfddj38gdddar0jfq0cz80kqb98xh3d37")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs @@ -11273,7 +12715,7 @@ with cell- and gene-level metadata.") r-matrix r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/scry.html") (synopsis "Small-count analysis methods for high-dimensional data") (description @@ -11288,13 +12730,13 @@ single-cell RNA-seq.") (define-public r-seqarray (package (name "r-seqarray") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SeqArray" version)) (sha256 (base32 - "0b0i17kwa8141y568k2asiv46hz4z0lwiqjz687d96j6kz3r3zgg")))) + "1a1vjkkr2bhzyjbark7n5wa8grxscwaaz8zpn0qlx7ybj66bvbgj")))) (properties `((upstream-name . "SeqArray"))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -11303,7 +12745,8 @@ single-cell RNA-seq.") r-genomicranges r-iranges r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-digest r-knitr r-matrix r-runit r-variantannotation)) (home-page "https://github.com/zhengxwen/SeqArray") (synopsis "Data management of large-scale whole-genome sequence variant calls") @@ -11318,18 +12761,18 @@ data access using the R programming language.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "154c3g4i6snsi8vkwjw4d8lyr3372d6vyw237nslw1y5n837yzir")))) + "0a5qndfdlsz38kwiijcshilwp6xiwlx0aqfx9ysw09a2kcb7hwww")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description @@ -11341,18 +12784,19 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0iv0dhs1z8i0jglh1iw6ypzh6qslnn5xly2kjfxaxk9cggnjb5h6")))) + "01dslqflyk7i30wlb2455xqq2zpyz91fg44q4fq6bbp9kj1npazm")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix)) + (native-inputs (list r-biocstyle r-bsgenome-drerio-ucsc-danrer7 r-runit)) (home-page "https://bioconductor.org/packages/seqPattern") (synopsis "Visualising oligonucleotide patterns and motif occurrences") (description @@ -11364,13 +12808,13 @@ reference point and sorted by a user defined feature.") (define-public r-sesame (package (name "r-sesame") - (version "1.22.2") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sesame" version)) (sha256 (base32 - "1d2vjglpbhmr4fjp3zwipf0nwj5pms4l9q1xngyxrsbr26x7jp1d")))) + "0s7vybr0nd5wx1qjkmfqjkff4wp9qv5ibk2fckzpwlsd2jv3pzng")))) (properties `((upstream-name . "sesame"))) (build-system r-build-system) (propagated-inputs (list r-biocfilecache @@ -11390,7 +12834,7 @@ reference point and sorted by a user defined feature.") r-summarizedexperiment r-tibble r-wheatmap)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/zwdzwd/sesame") (synopsis "Step-wise analysis of DNA Methylation BeadChips") (description @@ -11405,13 +12849,13 @@ and advanced quality control routines.") (define-public r-shinymethyl (package (name "r-shinymethyl") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "shinyMethyl" version)) (sha256 (base32 - "15r9x1fqladjviyisbhr8zff0a6g9kvbvx72xcp3bfadp3wpygds")))) + "1gbqyn55y1ybk4y67mj9vms6nzjhdx93ckrfyjkmispwra6drkmg")))) (properties `((upstream-name . "shinyMethyl"))) (build-system r-build-system) (propagated-inputs @@ -11422,7 +12866,7 @@ and advanced quality control routines.") r-minfi r-rcolorbrewer r-shiny)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/shinyMethyl") (synopsis "Interactive visualization for Illumina methylation arrays") (description @@ -11433,14 +12877,14 @@ methylation array data. Both the 450k and EPIC array are supported.") (define-public r-shortread (package (name "r-shortread") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0x5iqx2k2xs5rwjch0bpcb8pgc0nhb571991yahdr8hsxwbas3jm")))) + "0zqk40r6cvmwqh7izwi57hy4z2fgpfl7crpcpxyvpn7zf82fd8f8")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -11463,6 +12907,7 @@ methylation array data. Both the 450k and EPIC array are supported.") r-s4vectors r-xvector r-zlibbioc)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/ShortRead") (synopsis "FASTQ input and manipulation tools") (description @@ -11477,17 +12922,21 @@ ungapped alignment formats.") (define-public r-sictools (package (name "r-sictools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SICtools" version)) (sha256 - (base32 "0ymk18aj4r0526xqqkrvd75p4jrgrq2wshx7mqh2wj7nizjfn8fv")))) - (properties `((upstream-name . "SICtools"))) + (base32 "0jyycm82aw7xfx0h7ngd4nz4s8xfq7ky71nrvbj5m6jb3bkr4hjz")))) + (properties + `((upstream-name . "SICtools") + (updater-extra-inputs . ("ncurses")))) (build-system r-build-system) (arguments (list + ;; 1 test fails with a string mismatch. + #:tests? #false #:phases '(modify-phases %standard-phases (add-after 'unpack 'patch-curses @@ -11504,7 +12953,7 @@ ungapped alignment formats.") r-rsamtools r-stringr)) (inputs (list ncurses)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/SICtools") (synopsis "Find SNV/Indel differences between two bam files with near relationship") @@ -11517,23 +12966,59 @@ count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.") (license license:gpl2+))) +(define-public r-simona + (package + (name "r-simona") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "simona" version)) + (sha256 + (base32 "13qkca6ch7ppdf1clgzgnygh9zb05163bm5a402pya7wbq2vkdzx")))) + (properties + `((upstream-name . "simona") + (updater-extra-native-inputs + . ("r-go-db" "r-org-hs-eg-db" "r-proxyc")))) + (build-system r-build-system) + (inputs (list openjdk perl)) + (propagated-inputs (list r-circlize + r-complexheatmap + r-getoptlong + r-globaloptions + r-igraph + r-matrixstats + r-polychrome + r-rcpp + r-s4vectors + r-shiny + r-xml2)) + (native-inputs (list r-go-db r-knitr r-org-hs-eg-db r-proxyc r-testthat)) + (home-page "https://github.com/jokergoo/simona") + (synopsis "Semantic similarity on bio-ontologies") + (description + "This package implements infrastructures for ontology analysis by +offering efficient data structures, fast ontology traversal methods, and +elegant visualizations. It provides a robust toolbox supporting over 70 +methods for semantic similarity analysis.") + (license license:expat))) + (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.14.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "1031rkl2gcgx4k1biz4bc38hfq7r6diqk48769jhii0r06ablrhi")))) + "04ww535snhd6j6syqfabhi5yrphzlv9ydmvvvxpx5f8x2cai1cp9")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi - r-biocgenerics r-circlize r-clue r-cluster @@ -11543,13 +13028,10 @@ less than 2bp on both sides of indel region.") r-getoptlong r-globaloptions r-go-db - r-gosemsim - r-matrix - r-org-hs-eg-db - r-proxyc + r-simona r-slam r-tm)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jokergoo/simplifyEnrichment") (synopsis "Simplify functional enrichment results") (description "This package provides a new clustering algorithm, binary @@ -11561,13 +13043,13 @@ and comparing the clusterings.") (define-public r-singscore (package (name "r-singscore") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "singscore" version)) (sha256 (base32 - "12avzrc16mxz7v8jp4rxz5ia6008rjcja1h3hd0n60z644w9cng2")))) + "1yzpmchvkyaca18bybbmf29amh8pilf213gnl8in6cc3nr50f3hv")))) (properties `((upstream-name . "singscore"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11586,7 +13068,7 @@ and comparing the clusterings.") r-s4vectors r-summarizedexperiment r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://davislaboratory.github.io/singscore/") (synopsis "Rank-based single-sample gene set scoring method") (description @@ -11599,13 +13081,13 @@ level.") (define-public r-tcgautils (package (name "r-tcgautils") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAutils" version)) (sha256 (base32 - "0fmz1lfpn8ws584q4xlicg897qs36wgr78crw0d9415ci6qqb4r8")))) + "0zspiaj7s9ij466dl25k5lrr1r2gpav2dwpmzhqpqpm0pg436xpg")))) (properties `((upstream-name . "TCGAutils"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -11623,7 +13105,7 @@ level.") r-stringr r-summarizedexperiment r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/TCGAutils") (synopsis "TCGA utility functions for data management") (description @@ -11638,13 +13120,13 @@ identifier translation via the GDC API.") (define-public r-tkwidgets (package (name "r-tkwidgets") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tkWidgets" version)) (sha256 (base32 - "0k1d5r306mbry0h7yqp246i13adxlmxl2vhwdsfgh29v8qkg1szl")))) + "0s43wv4hg6g1x6li1w5zn4nvcyvhp013nh9p8b4b36mpij188lbj")))) (properties `((upstream-name . "tkWidgets"))) (build-system r-build-system) (propagated-inputs (list r-dyndoc r-widgettools)) @@ -11657,13 +13139,13 @@ identifier translation via the GDC API.") (define-public r-toast (package (name "r-toast") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TOAST" version)) (sha256 - (base32 "0srjx9z59a65nhrxbzxzxnkyn28zskc6z4p8drihq1lhw6mvdp4r")))) + (base32 "1iv9hfj9qijbvwcphm1l0syac8n7crb78sgb3b2pzvnzg5v71avn")))) (properties `((upstream-name . "TOAST"))) (build-system r-build-system) (propagated-inputs (list r-corpcor @@ -11695,13 +13177,13 @@ tissues. Current functionalities include (define-public r-trackviewer (package (name "r-trackviewer") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "trackViewer" version)) (sha256 (base32 - "01m0jwig3l6dfhd3w5aq4sx2krsipjg5jjxa78kalfrzrm6k05s4")) + "0qvan15w36ysby5688iz4kdimri2k16w318jgkynijiyg42i8y71")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "trackViewer"))) @@ -11728,10 +13210,8 @@ tissues. Current functionalities include r-grimport r-gviz r-htmlwidgets - r-igraph r-interactionset r-iranges - r-plotrix r-rhdf5 r-rsamtools r-rtracklayer @@ -11742,6 +13222,7 @@ tissues. Current functionalities include (native-inputs (list esbuild r-knitr + r-runit (origin (method url-fetch) (uri "https://web.archive.org/web/20230428092426id_/\ @@ -11761,13 +13242,13 @@ methylation data.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1lx11dyr8q4yd57l7rj0788488amhiiahfml2m69554hk94cd46i")))) + (base32 "00b4wgfvn8785l01vyx6n05l5lpngpk4gp5y2hpkcxrh49q19b45")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs @@ -11786,7 +13267,7 @@ methylation data.") r-rsamtools r-rtracklayer r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/transcriptR") (synopsis "Primary transcripts detection and quantification") (description @@ -11811,21 +13292,25 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "15q1mq48nclf2lqc2v769q79frrbm2l65d54vcqg06b861q2wq9h")))) + "10ldajw1a3naxy58w4zf9ri5ql93fd6r06cdwg2dyagsb8qg3l20")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-s4vectors r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-biocneighbors + r-delayedmatrixstats + r-knitr + r-testthat)) (home-page "https://bioconductor.org/packages/TrajectoryUtils") (synopsis "Single-cell trajectory analysis utilities") (description @@ -11838,14 +13323,14 @@ structures to hold pseudotime inference results.") (define-public r-trna (package (name "r-trna") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tRNA" version)) (sha256 (base32 - "0dg4s5kxsdh2j8smqi8vm7yncy9kb79sj8xlvf4wgf3aljarms21")))) + "1s8gqk8fcdxk4cg4l3p2h8hlw5bxwr793p5kjjax8n1gdywxzkhr")))) (properties `((upstream-name . "tRNA"))) (build-system r-build-system) @@ -11861,7 +13346,7 @@ structures to hold pseudotime inference results.") r-stringr r-structstrings r-xvector)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/tRNA") (synopsis "Analyzing tRNA sequences and structures") (description @@ -11875,13 +13360,13 @@ additional column data sets.") (define-public r-trnadbimport (package (name "r-trnadbimport") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tRNAdbImport" version)) (sha256 - (base32 "0yvgxxf5d5mh91cmbba66krj6jz5gl1qkgjck9310k4mk7pjfww3")))) + (base32 "10w0grspgd0781z84fpiam6h92j1mvlplpg9arrhlax1fkk4xbyj")))) (properties `((upstream-name . "tRNAdbImport"))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -11894,7 +13379,7 @@ additional column data sets.") r-structstrings r-trna r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-httptest r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/tRNAdbImport") (synopsis "Importing from tRNAdb and mitotRNAdb as GRanges objects") (description @@ -11905,13 +13390,13 @@ additional column data sets.") (define-public r-scds (package (name "r-scds") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scds" version)) (sha256 (base32 - "19xma4kmx8s6m6dvqyw461ahqyfqb7z3n5dz4ppab4xcpmqvx0vh")))) + "18k3665pndd4vgn5a67kmwxc9jkbngspl20qgdxn3y1hph8mbjw5")))) (properties `((upstream-name . "scds"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -11933,13 +13418,13 @@ scRNA-seq data computationally.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "055dylajbn94khi0829qhxx0lbn1pvh30xw09gjn1jvxsgzj49nc")))) + "0r9hhc23a3x9rm1ippx39llxfcagwbv70zn67wnyzvfyn93gbi3c")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -11950,7 +13435,7 @@ scRNA-seq data computationally.") r-summarizedexperiment r-trajectoryutils)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/slingshot") (synopsis "Tools for ordering single-cell sequencing") (description "This package provides functions for inferring continuous, @@ -12005,15 +13490,17 @@ tools either included in speaq or available elsewhere on CRAN.") (define-public r-spectra (package (name "r-spectra") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Spectra" version)) (sha256 (base32 - "0mvfndd7n7varrzmv9cd3ygwbdn97x5qcgmzcxc6hr76lnkwp8al")))) + "00jsmbkcwndm82aj6gc3qn0b48niajx8aymijy7cpq3vh6hlxpyr")))) (properties `((upstream-name . "Spectra"))) (build-system r-build-system) + ;; FIXME Tests fail with: Error in mzR::openMSfile(x): File NA not found + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocgenerics r-biocparallel r-fs @@ -12022,7 +13509,7 @@ tools either included in speaq or available elsewhere on CRAN.") r-mscoreutils r-protgenerics r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-mzr r-patrick r-testthat)) (home-page "https://github.com/RforMassSpectrometry/Spectra") (synopsis "Spectra infrastructure for mass spectrometry data") (description @@ -12037,17 +13524,17 @@ data sets ensuring a small memory footprint.") (define-public r-stager (package (name "r-stager") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "0ayjwv2i9q8dzq5pzhyzkxzkz9ycka2v6ccvq5y9cg7x0mw4qvbh")))) + (base32 "1rab6hcr8nwbpdlfy7c43dy66rwpj7vm0vvm95iislqrfjsc5pqi")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/stageR") (synopsis "Stage-wise analysis of high throughput gene expression data") (description @@ -12060,15 +13547,17 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.16.4") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "02fim09w9s38hvgp1g3fxqabd5r2fjysljlfrya2nr17drqkzqyx")))) + (base32 "118n30lq01xp7irdxffc5hmym7wini8pfsk2xszh8lwf9ii0l5z9")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) + ;; Tests attempt to connect to string-db.org website. + (arguments (list #:tests? #false)) (propagated-inputs (list r-gplots r-hash @@ -12079,6 +13568,7 @@ Biology at r-png r-rcolorbrewer r-sqldf)) + (native-inputs (list r-biocgenerics r-runit)) (home-page "https://git.bioconductor.org/packages/STRINGdb") (synopsis "Search tool for the retrieval of interacting proteins database") (description @@ -12093,13 +13583,13 @@ that integrates the various evidences.") (define-public r-structstrings (package (name "r-structstrings") - (version "1.20.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Structstrings" version)) (sha256 - (base32 "1ka9kixhgc9vfar18fzd8vd5ydmdkqa2s6xsmhlh927zrijs3vz9")))) + (base32 "02nzkn5iwqqixj92vyfazdxsv7j6hpzkn005gznv11kfkagv9hwn")))) (properties `((upstream-name . "Structstrings"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -12110,7 +13600,7 @@ that integrates the various evidences.") r-stringi r-stringr r-xvector)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/FelixErnst/Structstrings") (synopsis "Implementation of the dot bracket annotations with Biostrings") (description @@ -12127,13 +13617,13 @@ large extend by the @code{ViennaRNA} package.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "0hnpa6ykfasp2hshqdny29dyw6y9dib4rsm379fm7n8iami1rjp1")))) + (base32 "1b96zv2ny4anlxpxkda86cg65v8z13mf8h241if6aiks8pq0z7kr")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -12152,7 +13642,7 @@ large extend by the @code{ViennaRNA} package.") r-summarizedexperiment r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat r-tidyverse)) (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") (synopsis "R package designed to simplify structural variant analysis") (description @@ -12165,16 +13655,26 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "02cvgq2vgg0gz1gxkc4vnr9jg4wkj32bl5a1qyv77wnw2b2v5hp0")))) + "1kfkdn57crg9l00bpd2z4ads14nd9c2lh1m1lqbc6kszbxpq9185")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-test + (lambda _ + ;; This test requires r-txdb-hsapiens-ucsc-hg19-knowngene, but we + ;; can't add it due to a dependency cycle. + (delete-file + "inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R")))))) (propagated-inputs (list r-biobase r-biocgenerics @@ -12187,7 +13687,7 @@ involving two separate genomic loci encoded as GRanges objects.") r-s4arrays r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-annotate r-digest r-hgu95av2-db r-knitr r-runit)) (home-page "https://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") (description @@ -12200,13 +13700,13 @@ samples.") (define-public r-survcomp (package (name "r-survcomp") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "survcomp" version)) (sha256 (base32 - "090dl580cwicn3px1khkhcix25snig0k7phb7z3nzmrbxmp82ygc")))) + "10dia4ys97kka23jrdkaih9sm6azqnbnks1inmw4gr8q8h9jy9x8")))) (properties `((upstream-name . "survcomp"))) (build-system r-build-system) (propagated-inputs (list r-bootstrap @@ -12227,14 +13727,14 @@ of risk prediction (survival) models.") (define-public r-sva (package (name "r-sva") - (version "3.52.0") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "07iq894mf5d66cxjl283pcvj1frj56pb15z984d4svk6f5cacg3z")))) + "0syq6jsb6f2i3x47xr34n0k09bm1184sx0wnkh46v6jrfgbsh0qd")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -12243,6 +13743,8 @@ of risk prediction (survival) models.") r-limma r-matrixstats r-mgcv)) + (native-inputs + (list r-biocstyle r-bladderbatch r-pamr r-testthat r-zebrafishrnaseq)) (home-page "https://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -12258,16 +13760,18 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "13xxcqy5hhy45zglv6gc86ndmisfkjq4dg55x2j1kw3jqha1brnx")))) + "1f27vb03x1vmhi9nmizfzrvkyczhgrsgmc5fcf5xnyfmmhs97cnr")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) + ;; Tests fail because genWorkenvir fails to set up the environment. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocgenerics r-biostrings @@ -12283,7 +13787,7 @@ unmodeled, or latent sources of noise.") r-summarizedexperiment r-yaml)) (native-inputs - (list r-knitr)) + (list r-knitr r-systempiperdata r-testthat)) (home-page "https://github.com/tgirke/systemPipeR") (synopsis "Next generation sequencing workflow and reporting environment") (description @@ -12301,13 +13805,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "0ly4rai3na88dnfizsi60r6py0qmf0pw95b0hprfkvzpjyd72p75")))) + "1468m14b4hvabg2h14cbaayw34v4zmscn3fmmm37r4abamk7nh0m")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -12334,15 +13838,25 @@ dependencies between GO terms can be implemented and applied.") (define-public r-txdbmaker (package (name "r-txdbmaker") - (version "1.0.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "txdbmaker" version)) (sha256 - (base32 "1nl7lr0x0kicd44gvwrdslcnnlmqaf57rgp1gb22yvz3lfzjziqi")))) + (base32 "0k0clyrpw12b9x0nb4190lhdpd5gab4s1y645cpac66kcskc0j4p")))) (properties `((upstream-name . "txdbmaker"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests attempt to download files. + (for-each delete-file + '("inst/unitTests/test_makeTxDbFromUCSC.R" + "inst/unitTests/test_makeTxDbFromBiomart.R"))))))) (propagated-inputs (list r-annotationdbi r-biobase r-biocgenerics @@ -12359,7 +13873,7 @@ dependencies between GO terms can be implemented and applied.") r-rtracklayer r-s4vectors r-ucsc-utils)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-rmariadb r-runit)) (home-page "https://bioconductor.org/packages/txdbmaker") (synopsis "Tools for making TxDb objects from genomic annotations") (description @@ -12375,16 +13889,16 @@ convenient formats.") (define-public r-tximport (package (name "r-tximport") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0wayib05k976wivf9xgbfz5mfvi5hmxj3wm6zw031bj4w8dkc1v6")))) + "1rrnldicisjf2cjkvnynlsr91illi6v6wfyqn20xb10p947cyckl")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-readr r-testthat r-tximportdata)) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") (description @@ -12422,7 +13936,7 @@ of gene-level counts.") r-stringr r-tibble)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/rnabioco/valr") (synopsis "Genome interval arithmetic in R") (description @@ -12434,16 +13948,25 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0slvlhm65hkjspzlzs3gi04a6mlfwvda314z1nmzpdi3y5111fg7")))) + "0agkfdzs4nr2js94g1cnwxykc4f1678cfjx70r69gmy41s1ghybm")))) (properties `((upstream-name . "VariantAnnotation"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests depend on SIFT.Hsapiens.dbSNP132, which depends on + ;; r-variantannotation. + (delete-file "inst/unitTests/test_SIFTandPolyPhen.R")))))) (propagated-inputs (list r-annotationdbi r-biobase @@ -12463,7 +13986,9 @@ R, enabling interactive analysis and visualization of genome-scale data.") r-summarizedexperiment r-xvector r-zlibbioc)) - (native-inputs (list r-knitr)) + (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19 + r-knitr r-runit r-snpstats + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/VariantAnnotation") (synopsis "Package for annotation of genetic variants") (description "This R package can annotate variants, compute amino acid @@ -12473,19 +13998,19 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.72.0") + (version "3.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1r6cd92d4xlx4zdyy1sfaxicjf4q3arflmswpdkckkc4h9c6zf8m")))) + "0i0fghcrdgivm5amyx2clzqqx4yb3fq7s24v85jmclbsr8fnzm5q")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) (native-inputs - (list r-knitr)) ; for vignettes + (list r-biocstyle r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") (description @@ -12542,13 +14067,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "177yzqmkf3f2xgfrz1zpcw554yzm4njd2chhmvxi2vvijvnrgdf3")))) + (base32 "0x7gkx1ib6ggbr3dc97wxs52ph1chqcwqrn7xc4jmzs122gh52k0")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs @@ -12578,15 +14103,16 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "0laahd3v5m313q1iq259aikgqf7zlmpxyxhws2pr7vg97g37bbhs")))) + (base32 "1r4n5lnps47qrl90m5mm0i3530l0r31hd7hsp2d004sgbmyak304")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) + (native-inputs (list r-rcolorbrewer r-runit)) (home-page "https://git.bioconductor.org/packages/xmapbridge") (synopsis "Display numeric data in the web based genome browser X:MAP") (description @@ -12605,13 +14131,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.44.0") + (version "0.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "0fxv97m79w0ph4wbgp9drz6ahvnnzpv08grb11lr6a7laqq5x8s2")))) + "0dpnsvam6971b19xqlv1zniwjznya22jmffjpl4shz4sv8zin9nf")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -12623,10 +14149,10 @@ describing each of the graphs.") (substitute* "DESCRIPTION" (("zlibbioc, ") "")) (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) + (("import\\(zlibbioc\\)") ""))))))) (inputs (list zlib)) + (native-inputs (list r-runit)) (propagated-inputs (list r-biocgenerics r-iranges r-s4vectors r-zlibbioc)) (home-page "https://bioconductor.org/packages/XVector") @@ -12639,13 +14165,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "155q6983xjdjpq445lpg5n9gzf8gr18nll6dmjk7jwdq7fdxb602")))) + "0nz17g5dvj57c72csnpnfvylsq3z3c0qxvgsp7l2lcns9xc9rdnz")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -12659,15 +14185,17 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "1fyy3v1papg46cclk5fg8iqmg0671ccr82alvv41hk5d85ck04aq")))) + (base32 "1y1z2vjw04aq139a9f43s4kwl8zbx734s593cm15g0yxjsdpcgxv")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) + ;; This uses r-basilisk, which attempts to set up a Conda environment. + (arguments (list #:tests? #false)) (propagated-inputs (list r-basilisk r-cli @@ -12691,14 +14219,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "19znr3vwp20x84jiwy0im7s6vd8a71yng8w2ji88ffzq0xdkyyjm")))) + "1yvq6wa27q6r6m5zi9m9qqzqgxrndwybgz056yc5gpbngp1c2va7")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -12718,16 +14246,18 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "15icfcmpwrnjpyahc4v168fpcbsml6x7h4drmsyh9l8d1284yb4n")))) + "01zcbrk1yxv6jzainw4hc2c20mzg4ji8l8svbyncch39f3n6agb7")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) + ;; Some tests need pd.mapping50k.hind240, which needs this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-affyio r-biobase @@ -12742,6 +14272,7 @@ saving AnnData objects to disk.") r-rsqlite r-s4vectors r-summarizedexperiment)) + (native-inputs (list r-genomewidesnp6crlmm r-human370v1ccrlmm r-runit)) (home-page "https://bioconductor.org/packages/oligoClasses/") (synopsis "Classes for high-throughput arrays") (description @@ -12753,16 +14284,18 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.68.2") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0ch6b4rg5v6fj0fgniqiigx1gnnqgwji90bxqngllman388bx867")))) + "0z7y8sicap04alkqrzqdjiq7jnmk5mf9h1ki4622hw5wf0gjiark")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) + ;; Tests require r-oligodata, which depends on this package. + (arguments (list #:tests? #false)) (inputs (list zlib)) (propagated-inputs (list r-affxparser @@ -12777,7 +14310,7 @@ packages.") r-rsqlite r-zlibbioc)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description @@ -12789,13 +14322,13 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qfeatures (package (name "r-qfeatures") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QFeatures" version)) (sha256 (base32 - "1vd1kvx2kr47czz58375msc2x8p155cn0zqr4w7i1v1ki951r3a4")))) + "0c3zv42vb792pn74k1s3hxfhi6vp78nzfvmq5fwa4950bvhfp9s0")))) (properties `((upstream-name . "QFeatures"))) (build-system r-build-system) (propagated-inputs (list r-annotationfilter @@ -12813,7 +14346,7 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") r-summarizedexperiment r-tidyr r-tidyselect)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/RforMassSpectrometry/QFeatures") (synopsis "Quantitative features for mass spectrometry data") (description @@ -12827,13 +14360,13 @@ proteins) in a coherent and tractable format.") (define-public r-quantsmooth (package (name "r-quantsmooth") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantsmooth" version)) (sha256 - (base32 "1mgdrhq0j4b29l3y49h00ccwkz6vhs6hjb1236blmlzdf590q7gc")))) + (base32 "0nrlkp5gqmhxq7n2cjg7nxkdnc7rbb4cl79dfham0ky97pwisi4p")))) (properties `((upstream-name . "quantsmooth"))) (build-system r-build-system) (propagated-inputs (list r-quantreg)) @@ -12854,14 +14387,14 @@ on the location of the probe, and other useful tools.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1hgkrvbs1rf8db105ik9ar54zdx49v25hn71jgw7j5r43zngfg2a")))) + "0q9iafir09xnk2qgdaqhryd3y5kzcxcw9l0la1pnpanxdz2hl3i1")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -12909,13 +14442,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apcomplex (package (name "r-apcomplex") - (version "2.70.0") + (version "2.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apComplex" version)) (sha256 - (base32 "1fsqrds5r8bhdf7fbnw6rf3vqapl6xk1a5l6jjb98raxmjsrfyqs")))) + (base32 "0s8yg9rhi43v35l9hkp2fl7zk3rpn84rbwyn1l00l9fm3fr03qdm")))) (properties `((upstream-name . "apComplex"))) (build-system r-build-system) (propagated-inputs @@ -12934,13 +14467,13 @@ spectrometry} data.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "039my876v0k2mr50w90w3phj4cq55awf5ks07kr2fnm7w211gxvs")))) + "1xzh8p4ybal3m4rfpja5qnnqd8hqbszppkxfqf7rm4z2kz2ga25q")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -12950,7 +14483,7 @@ spectrometry} data.") r-rcppeigen r-rcppnumerical r-summarizedexperiment)) - (native-inputs (list r-knitr r-rmarkdown)) + (native-inputs (list r-knitr r-rmarkdown r-testthat)) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for @@ -12961,13 +14494,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "0dj3pcycnjll8z1r61l6gnjvq74w2l0glrx6hqwcqvk5j7ixcdz7")))) + "0annhgzl4b5ykn0993zdqlcxppbrrn8rcxivfkjhdqmq41r4n4bm")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -12979,6 +14512,7 @@ posterior for individual coefficients.") r-rsamtools r-rtracklayer r-summarizedexperiment)) + (native-inputs (list r-biocstyle r-runit)) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high @@ -12988,16 +14522,20 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1sr0zy5pbjmjzkwkpjmr26k4dcf3f3kxsl7z2nqw0p0a14rh57pm")))) - (properties `((upstream-name . "DiffBind"))) + "1whb4k54wm21k74r6qyng130nnaii9czh9dhvl1x7hnqa8gq0dx7")))) + (properties + `((upstream-name . "DiffBind") + (updater-extra-native-inputs . ("r-biocstyle")))) (build-system r-build-system) + ;; Vignettes fail with: "Only one peakset meets specified criteria." + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-amap r-apeglm @@ -13022,6 +14560,7 @@ signal in the input, that lead to spurious peaks during peak calling.") r-s4vectors r-summarizedexperiment r-systempiper)) + (native-inputs (list r-biocstyle r-testthat r-xtable)) (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description @@ -13066,13 +14605,13 @@ processing to visualization and annotation.") (define-public r-mbecs (package (name "r-mbecs") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MBECS" version)) (sha256 - (base32 "15nv5rbw158d071gscms6p42wzf6ibnabiqcq256rcz6j0r69b63")))) + (base32 "0b8apb9gybapl9dnc7h6f0kk4ra35wsypr9gr83hbjp85wwv8glc")))) (properties `((upstream-name . "MBECS"))) (build-system r-build-system) (arguments @@ -13100,7 +14639,7 @@ processing to visualization and annotation.") r-tibble r-tidyr r-vegan)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/rmolbrich/MBECS") (synopsis "Evaluation and correction of batch effects in microbiome data-sets") @@ -13116,16 +14655,16 @@ before and after correcting for batch effects.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "0fnf6ymbcfchhlcbwpwlcq1jc3lfzh9f8mf76xfy7vrpwngds1fs")))) + "0alm36lj0p541wyrk85ddyk8g4sscip54532i8pkb6a8mclp9cp3")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (propagated-inputs (list r-beachmat r-benchmarkme @@ -13148,13 +14687,13 @@ large datasets, including support for on-disk data representation.") (define-public r-multibac (package (name "r-multibac") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiBaC" version)) (sha256 - (base32 "0m08620sii9181y0vlcrw9nbcnp4vnjjxvp96iqlgg5fsb23wbl7")))) + (base32 "0bg9jgkrb16g6xxvw1acqc0ydwljwk1zvx3zh597893jifsx0b45")))) (properties `((upstream-name . "MultiBaC"))) (build-system r-build-system) (propagated-inputs @@ -13178,14 +14717,14 @@ the batches considered.") (define-public r-multtest (package (name "r-multtest") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "04dv5rcqwpv0im7j3hvcj8hjybgs4a384zgnjyqbcipcicd2rjz4")))) + "00gs0mb371x5aj9wa8infwfpmg3iqyz0bgmn6gk9mcfl9rf6xkfk")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-mass r-survival)) @@ -13213,17 +14752,26 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1wa10s9a8p6lajim1lbw4rxyc4fz7y6fpymrh0c0ip85971cd9hv")))) + "0fq7nbbcpmyhzhahgxdz8dx2bbzzv5cidd6gs7sr5i5184iyq2wp")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-bad-test + (lambda _ + ;; This one test fails for unknown reasons. + (substitute* "inst/unitTests/graphNEL_test.R" + (("checkEquals\\(\"not a node:.*") ""))))))) (propagated-inputs (list r-biocgenerics)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit r-xml)) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description @@ -13256,13 +14804,13 @@ fitting of some classes of graphical Markov models.") (define-public r-ggtreeextra (package (name "r-ggtreeextra") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtreeExtra" version)) (sha256 (base32 - "1wy229rnp356hi144flm9fvhv414jxmxc967f7pyqwl4abiwlmzm")))) + "1xlwz45zcr51r7n2yc2ffxz0p4xgwhnka868crg17f9d9g6phhdr")))) (properties `((upstream-name . "ggtreeExtra"))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -13272,7 +14820,7 @@ fitting of some classes of graphical Markov models.") r-magrittr r-rlang r-tidytree)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/YuLab-SMU/ggtreeExtra/") (synopsis "Add geometric layers On circular or other layout tree of ggtree") @@ -13316,7 +14864,7 @@ rectangular layout tree built by ggtree with the grammar of ggplot2.") r-summarizedexperiment r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/cafferychen777/ggpicrust2") (synopsis "Make PICRUSt2 output analysis and visualization easier") (description @@ -13356,13 +14904,13 @@ a given recall, F-score for single and multiple classes are available.") (define-public r-pepsnmr (package (name "r-pepsnmr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PepsNMR" version)) (sha256 (base32 - "0z3kw8j972zmrcyikag5js20zpgc3l5bgkn5q31dzi1q7ynpkwhv")))) + "03sipcga9gmcypryq3c0lhvdp1dzgbjfzxldrrp2ycyjwzwr9wzn")))) (properties `((upstream-name . "PepsNMR"))) (build-system r-build-system) (propagated-inputs @@ -13398,7 +14946,7 @@ signals directly in the Bruker format.") (build-system r-build-system) (propagated-inputs (list r-codetools r-graph r-xml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-rgraphviz r-runit)) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description @@ -13413,14 +14961,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.38.1") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "11mswd6y4c8l0adrpc4z8hh96dcx59bf70zy572r5lfsj8rz0rgk")))) + "0zzpmrni4la6d2zws8wxak51lnn9g2i9xbwj1f3micpyn1bxlsc9")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -13457,7 +15005,17 @@ determining dependencies between variables, code improvement suggestions.") r-universalmotif r-venndiagram)) (native-inputs - (list r-knitr)) + (list r-biomart + r-bsgenome-celegans-ucsc-ce10 + r-bsgenome-drerio-ucsc-danrer7 + r-bsgenome-hsapiens-ucsc-hg19 + r-ensdb-hsapiens-v79 + r-knitr + r-org-ce-eg-db + r-org-hs-eg-db + r-reactome-db + r-testthat + r-txdb-hsapiens-ucsc-hg38-knowngene)) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description @@ -13474,18 +15032,19 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1r7n5p89460h47mnfh190184dbcmrbj0j5d7dswkfwh6ixan3zyc")))) + "132cd7qw3rqnv20raf0n1bnjvmkfckg928p80iflj576wxhwcndk")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) (propagated-inputs (list r-matrixstats)) + (native-inputs (list r-testthat)) (home-page "https://bioconductor.org/packages/MatrixGenerics") (synopsis "S4 generic summary statistic functions for matrix-like objects") (description @@ -13501,12 +15060,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1h96aq92bad69ycrmrvxwdz8dg9rk44925gj83gxzqypw88j2x0y")))) + (base32 "0j4hib9x4zr40k6gs911vvj766b7f46n15jpq8p2lv89jrh8wa99")))) (build-system r-build-system) (propagated-inputs (list r-limma)) @@ -13520,12 +15079,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1fz39fdkfvfhzm69pfvliqvp48wsldwm3kpgbsaacrdh46jg5vzk")))) + (base32 "0gcw2765ljqnhvnmawxhcz8xrfrjvh9slsaqhy8ggzhr47g7xnb6")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -13539,12 +15098,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1gjd3ggiw93cwcacjb1472ia98aaapj9gln04v5pbwmp2r4xfcs7")))) + (base32 "178gi1d0mdm201ay1srikndd6dsbi41rmn8h3rvmv3q2ngzk70hm")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -13558,12 +15117,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1myk6qgl45ya7qw6sx6xc98d8m5ffl2ghm3zvqmyh9r0sp6x184f")))) + (base32 "06ips85m2yrp7iwqm1l9hxkr3d5ny3myhjr8dkyhmw819gvdfhq8")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -13577,6 +15136,7 @@ the @code{arrayCGH} packages.") r-matrixstats r-r-utils r-rsamtools)) + (native-inputs (list r-biocstyle)) (home-page "https://bioconductor.org/packages/QDNAseq") (synopsis "Quantitative DNA sequencing for chromosomal aberrations") (description "The genome is divided into non-overlapping fixed-sized bins, @@ -13590,14 +15150,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "0nlkynzijxl6f8983vdpmcssvrpjf6s42zx3lxfwxwlhrvz1yg9l")))) + "0vhp9agxqkfm7fs07kkd9gqzp4v7936wdmbd2qc2gf4g3rw3akzm")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -13614,14 +15174,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "013lmgdkj596gqzm0nlxjqpv0w94hap9vndp5znqpk4inq88gj8m")))) + "1pbzqldavg21zds4v9yvhfdf0knli7z66xldsmdz646v6f1q1579")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -13635,6 +15195,7 @@ more complex hypotheses) via empirical Bayesian methods.") r-rsamtools r-rtracklayer r-s4vectors)) + (native-inputs (list r-biocstyle r-runit)) (home-page "https://bioconductor.org/packages/ChIPComp") (synopsis "Quantitative comparison of multiple ChIP-seq datasets") (description @@ -13648,14 +15209,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "0h0sxmg4knsarh7w7dnp539cs9sfxjw4413q1yyyz3gbi23bzww4")))) + "1lw88kw3wqzqb5ahq6p9zchqbkq7f2hm8djngq1r81ydjdmnih3p")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -13676,7 +15237,7 @@ datasets.") r-s4vectors r-sqldf)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the @@ -13689,14 +15250,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "0p0q28n8hlai80pxxns9pzzg552pbwlxlph8zjf78bwbjagrfbz5")))) + "1xxar40bqmawz07h3l6r8m03cq65yymmcc9vyyk66c28yfr46crw")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -13708,6 +15269,7 @@ assessment, principal component analysis on codon coverage.") r-rsamtools r-s4vectors r-seqlogo)) + (native-inputs (list r-biocstyle r-runit)) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") (description @@ -13718,14 +15280,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0ikkmhz6grmhksmyypj9hqmblls4cgww0dx4kzg4cy5bpavsq1hs")))) + "15mvpd64hhgwc30m7ayd60bc1icmrgchpjp21dxpw2za5r4162kq")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -13739,7 +15301,7 @@ parsing of genetic sequencing data from ribosome profiling experiments.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description @@ -13752,14 +15314,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "16aaaa4nr1y5ng1hzw87q950clid28iqf4gkypcpihg3cz69axxg")))) + "1p3dcpm8bggxxiqzx238dvv3nyybg9agy6i1k7ngdvrxr6zlb0c8")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -13781,7 +15343,7 @@ experiments.") r-s4vectors r-stringr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") (synopsis "R package for handling genomic interaction data") (description @@ -13793,14 +15355,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "09whaam2r30dq8y9r6vvc0r4sisz78c921bgx7wj6cmn2nvpgf9q")))) + "1k2s1kjcbj4gkpj3fbb1gk2apg8b4anybgdhaw4s0w5ximy69mp7")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") @@ -13813,22 +15375,25 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0bc7dcpz0agbc42f8agf05amyhpavz55fdp622if5af5dn1ww6pr")))) + "1paya44vvzvbv0mr0vky4sjvmaqx8y4n5p457vxy2b8b3l086p45")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biasedurn r-biocgenerics r-genelendatabase + r-genomeinfodb + r-genomicfeatures r-go-db - r-mgcv)) + r-mgcv + r-rtracklayer)) (home-page "https://bioconductor.org/packages/goseq/") (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") (description @@ -13839,68 +15404,82 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1d7rq3irp3n0fabfgjs2x2c9lscz70a38qf3wbxvi417qn7fpyla")) + "0jqgk8bb7izblhfpjdqkf12jmhkmpwj8sv07429jrxvlj3c84k7a")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib/" (for-each delete-file ;; XXX: we keep inst/v1/js/glimma.min.js because ;; it's not clear how to build it. - (cons "vega/vega.min.js" - (find-files "datatables" - "\\.min\\.js$"))))))) + (cons* "vega/vega.min.js" + "jquery/jquery-3.6.1.min.js" + (find-files "datatables" + "\\.min\\.js$"))))))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (arguments (list - #:modules '((guix build utils) - (guix build r-build-system) - (srfi srfi-1)) + #:modules + '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (srfi srfi-1) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) #:phases - '(modify-phases %standard-phases + '(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" - (let ((files (list "datatables/Buttons-1.6.1/js/buttons.bootstrap.js" - "datatables/Buttons-1.6.1/js/buttons.bootstrap4.js" - "datatables/Buttons-1.6.1/js/buttons.colVis.js" - "datatables/Buttons-1.6.1/js/buttons.flash.js" - "datatables/Buttons-1.6.1/js/buttons.foundation.js" - "datatables/Buttons-1.6.1/js/buttons.html5.js" - "datatables/Buttons-1.6.1/js/buttons.jqueryui.js" - "datatables/Buttons-1.6.1/js/buttons.print.js" - "datatables/Buttons-1.6.1/js/buttons.semanticui.js" - "datatables/Buttons-1.6.1/js/dataTables.buttons.js" - "datatables/DataTables-1.10.20/js/dataTables.bootstrap.js" - "datatables/DataTables-1.10.20/js/dataTables.bootstrap4.js" - "datatables/DataTables-1.10.20/js/dataTables.foundation.js" - "datatables/DataTables-1.10.20/js/dataTables.jqueryui.js" - "datatables/DataTables-1.10.20/js/dataTables.semanticui.js" - "datatables/DataTables-1.10.20/js/jquery.dataTables.js" + (let ((files (list "datatables/Buttons-2.3.3/js/buttons.bootstrap.js" + "datatables/Buttons-2.3.3/js/buttons.bootstrap4.js" + "datatables/Buttons-2.3.3/js/buttons.bootstrap5.js" + "datatables/Buttons-2.3.3/js/buttons.bulma.js" + "datatables/Buttons-2.3.3/js/buttons.colVis.js" + "datatables/Buttons-2.3.3/js/buttons.dataTables.js" + "datatables/Buttons-2.3.3/js/buttons.foundation.js" + "datatables/Buttons-2.3.3/js/buttons.html5.js" + "datatables/Buttons-2.3.3/js/buttons.jqueryui.js" + "datatables/Buttons-2.3.3/js/buttons.print.js" + "datatables/Buttons-2.3.3/js/buttons.semanticui.js" + "datatables/Buttons-2.3.3/js/dataTables.buttons.js" + "datatables/DataTables-1.13.1/js/dataTables.bootstrap.js" + "datatables/DataTables-1.13.1/js/dataTables.bootstrap4.js" + "datatables/DataTables-1.13.1/js/dataTables.bootstrap5.js" + "datatables/DataTables-1.13.1/js/dataTables.bulma.js" + "datatables/DataTables-1.13.1/js/dataTables.dataTables.js" + "datatables/DataTables-1.13.1/js/dataTables.foundation.js" + "datatables/DataTables-1.13.1/js/dataTables.jqueryui.js" + "datatables/DataTables-1.13.1/js/dataTables.semanticui.js" + "datatables/DataTables-1.13.1/js/jquery.dataTables.js" "datatables/JSZip-2.5.0/jszip.js" - "datatables/Scroller-2.0.1/js/dataTables.scroller.js" - "datatables/Scroller-2.0.1/js/scroller.bootstrap.js" - "datatables/Scroller-2.0.1/js/scroller.bootstrap4.js" - "datatables/Scroller-2.0.1/js/scroller.foundation.js" - "datatables/Scroller-2.0.1/js/scroller.jqueryui.js" - "datatables/Scroller-2.0.1/js/scroller.semanticui.js" + "datatables/Scroller-2.0.7/js/dataTables.scroller.js" + "datatables/Scroller-2.0.7/js/scroller.bootstrap.js" + "datatables/Scroller-2.0.7/js/scroller.bootstrap4.js" + "datatables/Scroller-2.0.7/js/scroller.bootstrap5.js" + "datatables/Scroller-2.0.7/js/scroller.bulma.js" + "datatables/Scroller-2.0.7/js/scroller.dataTables.js" + "datatables/Scroller-2.0.7/js/scroller.foundation.js" + "datatables/Scroller-2.0.7/js/scroller.jqueryui.js" + "datatables/Scroller-2.0.7/js/scroller.semanticui.js" "datatables/datatables.js" - "datatables/jQuery-1.12.4/jquery-1.12.4.js" "vega/vega.js"))) (for-each (lambda (source) - (let ((target (string-append (basename source ".js") ".min.js"))) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target)))) - files)))))))) + (let ((target (string-append (dirname source) "/" (basename source ".js") ".min.js"))) + (minify source #:target target))) + files) + (let ((source (assoc-ref inputs "js-jquery")) + (target "jquery/jquery-3.6.1.min.js")) + (minify source #:target target))))))))) (propagated-inputs (list r-deseq2 r-edger @@ -13910,7 +15489,17 @@ defined categories which are over/under represented in RNA-seq data.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list esbuild r-knitr)) + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("r-pryr" ,r-pryr) + ("r-testthat" ,r-testthat) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-3.6.1.js") + (sha256 + (base32 + "1lm4zcpvqdi7qi2s7bgci2z74wazq0z0bdvjmlrqbhmfrpk42ffz")))))) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -13924,13 +15513,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "1my8v0zx5xsxjf8dj2yw92b8zp725hxhb2vrl5ccgz2w9xkn0dkj")))) + "141drlbgld05npk1bay7pcng7xmm43y26559qs8mxy9432cpzx9n")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -13945,9 +15534,11 @@ information.") r-rcpparmadillo r-rlang r-singlecellexperiment + r-sparsearray r-summarizedexperiment r-vctrs)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-biocparallel r-knitr r-limma r-mass r-scran r-testthat r-zoo)) (home-page "https://github.com/const-ae/glmGamPoi") (synopsis "Fit a Gamma-Poisson Generalized Linear Model") (description @@ -13960,18 +15551,19 @@ experiments.") (define-public r-rots (package (name "r-rots") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "1s9hr64gpz08j638wlglcmk6c8yyj1hzrgddiphklkapc1asr320")))) + "16prf1kwkgqcal37jhk4s3hz6yzlklxwm2clsmw8jf74n0igp0x0")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://bioconductor.org/packages/ROTS/") (synopsis "Reproducibility-Optimized Test Statistic") (description @@ -13983,14 +15575,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0my4jpxw3xy9n40cqvdaz6ay7gpwshn2iqxr43knrk0ckpyxx2cr")))) + "1d2v7wqcdabr2903pi36il0hhkq1fr2fw0b8gznn89yyfgwq9k4a")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) @@ -14007,13 +15599,13 @@ genes or proteins in these datasets.") (define-public r-plyranges (package (name "r-plyranges") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plyranges" version)) (sha256 (base32 - "0rh5l6bd80nhffqpnnc2c00mvp8p32ykld05h94c3y8c9mvmsl58")))) + "0ai6p7q4iva420wnm0008p1vivd72gc1anwhzzsmy14bxr52rwbx")))) (properties `((upstream-name . "plyranges"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -14028,7 +15620,7 @@ genes or proteins in these datasets.") r-rtracklayer r-s4vectors r-tidyselect)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/plyranges") (synopsis "Fluent interface for manipulating GenomicRanges") (description @@ -14041,14 +15633,14 @@ accessiblity for new Bioconductor users is hopefully increased.") (define-public r-inspect (package (name "r-inspect") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0147ss218d3dnqbdgfwsg24an63qln8l5kkv0y4hm56bncdrm1i0")))) + "1w5w5vcdf2i7dzss05z2h32fis9w3ivg1jixcviwsavk4k5bvwdb")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -14087,14 +15679,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0vxxg6fkgck640p9plk4vx3d05794s3xgxksv819d2wicvyby4hk")))) + "0pppm937415xsmw0g39022lr07x3551ki6h11p8d7cpwbjmym44f")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -14114,14 +15706,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0i91kjwransy6l217rmxfzfchb43h1sjk8ygf0y8a3rv6rp7ylfd")))) + "0218z7g8c48lhpgd98kpsqph4pa4pdq35lkpwsbhh9l3bzn4db17")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -14139,20 +15731,20 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.22.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1krg4cs406ymk27qcj3j1jsl8vl4j9k5zvwf4vzxgbw3x6lpywid")))) + "1k8jiypfv8gqrkgp51kjb3h0n0ddd8y84rg9jijyxzldqslgcak3")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors)) + (list r-assorthead r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description @@ -14167,19 +15759,19 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0c6sp5nps31ygrr7lxxc2gbg19qsk107v23x8f6acqk1xwlsfppi")))) + "1qkxwpxbcxqk2yifpbqgywrd1vsf53s8bckcfgj7zdh124xhwjwj")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs (list r-delayedarray r-matrix r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/LTLA/ScaledMatrix") (synopsis "Create a DelayedMatrix of scaled and centered values") (description @@ -14193,16 +15785,28 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "0xfjq13yirfz7dzzlf2m60lk8xb3qh6k5hr66ygvjnm716x3vyh1")))) + "0x1fd3422icp56ac01dn5nk5y04724sv80pb24fd993d426jj1xj")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Some tests need r-ggtree, which depends on this package. + (for-each delete-file + '("tests/testthat/test-conversion.R" + "tests/testthat/test-merge-tree.R" + "tests/testthat/test-tree-subset.R" + "tests/testthat/test-treedata-accessor.R"))))))) (propagated-inputs (list r-ape r-dplyr @@ -14212,7 +15816,7 @@ multiplication.") r-tibble r-tidytree r-yulab-utils)) - (native-inputs (list r-knitr)) + (native-inputs (list r-igraph r-knitr r-testthat r-xml2)) (home-page "https://github.com/YuLab-SMU/treeio") (synopsis "Base classes and functions for Phylogenetic tree input and output") (description @@ -14226,13 +15830,13 @@ platform for merging tree with associated data and converting file formats.") (define-public r-treesummarizedexperiment (package (name "r-treesummarizedexperiment") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TreeSummarizedExperiment" version)) (sha256 (base32 - "0ygzw9nba5pxgrbib8sm7qwhzzm8m038banb0z7n42vkb1cb3d5i")))) + "187dbjb1w45v2gx510yk28hxvhc1bdjz5l853kmxdpr4wxs7nh4z")))) (properties `((upstream-name . "TreeSummarizedExperiment"))) (build-system r-build-system) (propagated-inputs @@ -14247,7 +15851,7 @@ platform for merging tree with associated data and converting file formats.") r-singlecellexperiment r-summarizedexperiment r-treeio)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/TreeSummarizedExperiment") (synopsis "S4 class for data with tree structures") (description @@ -14259,14 +15863,14 @@ data.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "1bm7c46k8qbajjvl8475b7fcd0dvg9s1bir8313qgm466qm6immh")))) + "0ki9cap34jbf2xa9xkddfmaj8lmf5vc6b3a0w03q3z8c465v06g5")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -14284,7 +15888,7 @@ data.") r-tidytree r-treeio r-yulab-utils)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://yulab-smu.top/treedata-book/") (synopsis "R package for visualization of trees and annotation data") (description @@ -14297,20 +15901,20 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "100wsg2y7069r7xk5bsk5n4n8dqvpbk297w5ishnijrvxhbs9f8n")))) + "1ysdgnyzn5n2fazmx2az5kk30n10xla3l9xhrik3mmmif0ix0p8l")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/metapod") (synopsis "Meta-analyses on p-values of differential analyses") (description @@ -14326,18 +15930,27 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1xl9wn3slj3ywjglb8zq2p0ifx4xwxbqsm99fjlf6hanfhmnxyay")))) + "17flxapf8jw44rsbfz0iifhn6kdb2248lppbq0iz9c021wxlk28h")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; 4 tests fail with "Objects equal but not identical". + (delete-file "tests/testthat/test-lowrank.R")))))) (propagated-inputs - (list r-beachmat + (list r-assorthead + r-beachmat r-biocgenerics r-biocparallel r-delayedarray @@ -14348,7 +15961,7 @@ missing values and weighting where appropriate.") r-s4vectors r-scaledmatrix)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description @@ -14394,7 +16007,7 @@ possible, parallelization is achieved using the BiocParallel framework.") r-tidyr r-tidyselect r-vim)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion @@ -14415,8 +16028,11 @@ maps.") "13wiw7isdmpwhynxjrhimy9yglcz1108k7nwa98vq9czq49zpada")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) + ;; Disable vignettes because they use a removed function in r-ggplot2. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml)) + (native-inputs (list r-testthat)) (home-page "https://github.com/bcalder/savR") (synopsis "Parse and analyze Illumina SAV files") (description @@ -14427,14 +16043,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "0y39fpbnykqf5ycpi9q3rw73dkn2ksll7n6nafimxvxsh463d8ky")))) + "0xmznc8cc6nphzr5gkc4cccix80d5397qnqwx6q7imdfbm0ygy8i")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -14456,7 +16072,7 @@ Viewer (SAV) files, access data, and generate QC plots.") r-scales r-viridis)) (native-inputs - (list r-knitr)) + (list r-chipexoqualexample r-knitr r-testthat)) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description @@ -14487,14 +16103,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1q4s6rb6iv9cmfkjymgdyb4h3z0x0kzzd2bvfdjrzzzza6vhjpxl")))) + "1ckbj338brcsj5kx5w0xs1gh8j3mx41b55lzf48irvfnslxk3iws")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -14509,13 +16125,13 @@ abnormal copy number.") (define-public r-hmmcopy (package (name "r-hmmcopy") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HMMcopy" version)) (sha256 - (base32 "1i2n4i4vkxqfgdcmwhz1vcbhxk716m1blc2drzh5449y6x3qd026")))) + (base32 "169hxg2cnhc48gfyz2rag1ahs2q1slp70v89bvzibkn00srclgk5")))) (properties `((upstream-name . "HMMcopy"))) (build-system r-build-system) (propagated-inputs (list r-data-table)) @@ -14609,14 +16225,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "1lbvrw6fcjhrm6v71lmnphv4hbdh03czgx3822ckdk6xrvyh54cf")))) + "0hhs265p6y2118wmp5h8lp1b60d6vl27lb8fv12b0jfmln8ninzl")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -14626,6 +16242,7 @@ and regression inferences from RNA-sequencing data.") r-rcpp r-rcppeigen r-testthat)) + (native-inputs (list r-testthat)) (home-page "https://bioconductor.org/packages/EBSeq") (synopsis "Differential expression analysis of RNA-seq data") (description @@ -14636,13 +16253,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "1g4pms5dcr4cdb47gr9kw3mc06v890b38zrsapd4x1cqhgfbgjyg")))) + "0cr1lb6na4s3ggh5516sclg08n74kvifgb5yyy1mijzryf9yrzcl")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -14661,7 +16278,7 @@ gene and isoform level using RNA-seq data") r-s4vectors r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and @@ -14674,14 +16291,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "1wcjmw655k389ph61v3gxjv7gk2q70h25zmdzvd4ggbxg8vh2mp1")))) + "0w4rwj2vprpayijjwlqrximxlr8dnc1zs9pmr2wil7r76zvxlf94")))) (build-system r-build-system) (arguments (list @@ -14712,7 +16329,7 @@ coordinates.") (list zlib)) (native-inputs (append - (list pkg-config r-knitr) + (list gfortran pkg-config r-knitr r-testthat) (if (or (target-aarch64?) (target-riscv64?)) (list config) @@ -14733,20 +16350,20 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0j7rfyhpzr8zzyvjyphlfviy07z30nzsqq6isi4l0r4qgaziy1s6")))) + "1dwzwv3y9shy2fxm8ni1ai0v86fh74g4fml6p4x38pwkbxcc6qn6")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-fdrtool r-lpsymphony r-slam)) (native-inputs - (list r-knitr)) + (list r-ggplot2 r-knitr r-scales r-testthat)) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description @@ -14762,14 +16379,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1m3awsz8h3gbi82an73kbxcsch2gl737zaanckl1vq2ghymqykrp")))) + "0fhvzrp6q4kcx9xjy96iyra2z1yc4c2vagmnymzbj1gli4sl2idx")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -14787,7 +16404,7 @@ independent of the p-value under the null hypothesis.") r-shinydashboard r-upsetr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description @@ -14800,21 +16417,21 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1zq75i20kv0lgnh19zbhw5khxrag627ynqjvh3rj5kxbhj1l2z7c")))) + "0kxazkh6hz1x5jj1j2n3rww3jknb4nmgj8pjmj3jpqq0sb1gf292")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) (propagated-inputs (list r-delayedarray r-matrix r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/LTLA/ResidualMatrix") (synopsis "Create a DelayedMatrix of regression residuals") (description @@ -14829,16 +16446,26 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1h70rm0h711ndj9kz3q10yd9f6npjiwvk9wmkg6w3pdgjni1nrl0")))) + "0l63w2c2jl27rj47604lx80wlppsp7h1panbm0n89fvf4vbzgm22")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Two tests fail with: Objects equal but not identical + (for-each delete-file + '("tests/testthat/test-correct-exps.R" + "tests/testthat/test-reduced-mnn.R"))))))) (propagated-inputs (list r-beachmat r-biocgenerics @@ -14855,8 +16482,9 @@ multiplication and calculation of row/column sums or means.") r-scaledmatrix r-scuttle r-singlecellexperiment + r-sparsearray r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-bluster r-knitr r-scran r-testthat)) (home-page "https://bioconductor.org/packages/batchelor") (synopsis "Single-Cell Batch Correction Methods") (description @@ -14872,14 +16500,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1k8an0ifcgx54lqzpim3q37y4rhv57i94i46dlpmdyfghqqw0fny")) + "0fn50b4yxsslgvw8l6zfbxr4bl8hd9rb7p3dggw040hfm8gadgl9")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "MAST"))) @@ -14918,7 +16546,8 @@ the numbers of cells across batches.") (sha256 (base32 "17c3a1hqc3ybwj7hpw8prazajp2x98aq7nyfn71h6lzjvblq297g")))) - ("r-knitr" ,r-knitr))) + ("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat))) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -14929,15 +16558,26 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "0b09mf9fph0mb0zing0prc757d223858q9lj4j3kfpfjpd3jffai")))) + "1qxf83zblihxm3fs5zrzf1spzhnm332n6nbzbzaid69l7xmgl5x0")))) (build-system r-build-system) + (arguments + (list + ;; Test files are not included. + #:tests? #false + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "inst/tests/basic_tests.R" + (("^load_small_test" m) + (string-append "library(testthat)\n" m)))))))) (propagated-inputs (list r-biobase r-biocgenerics @@ -14969,7 +16609,7 @@ single cell assay data.") r-vgam r-viridis)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description @@ -15003,7 +16643,7 @@ qPCR data, but could be used with other types as well.") (inputs (list zlib)) (native-inputs - (list gfortran)) + (list gfortran r-knitr r-testthat)) (propagated-inputs (list r-igraph)) (home-page "https://github.com/cole-trapnell-lab/leidenbase") @@ -15019,17 +16659,17 @@ several functions from the R igraph package.") (define-public r-sangerseqr (package (name "r-sangerseqr") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sangerseqR" version)) (sha256 (base32 - "01z2b7950yxhv8p73rfmq84bscrlpl956ihfyarnzdq9v9ljzzd9")))) + "1xvwlnyrs5w3aiapbiiq8dx71hf7803fywbqhg7nvqkdbls5iljd")))) (properties `((upstream-name . "sangerseqR"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-pwalign r-shiny r-stringr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/sangerseqR") (synopsis "Tools for Sanger Sequencing data in R") (description @@ -15056,8 +16696,17 @@ basecalls and plotting chromatograms.") (base32 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Two tests fail with: Objects equal but not identical + (delete-file "tests/testthat/test_calibration.R")))))) (propagated-inputs (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) + (native-inputs (list r-ggplot2 r-testthat)) (home-page "https://pneuvial.github.io/sanssouci") (synopsis "Post Hoc multiple testing inference") (description @@ -15067,82 +16716,104 @@ user-defined and/or data-driven sets of hypotheses.") (license license:gpl3)))) (define-public r-monocle3 - (package - (name "r-monocle3") - (version "1.0.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/cole-trapnell-lab/monocle3") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) - (build-system r-build-system) - (propagated-inputs - (list r-assertthat - r-batchelor - r-biobase - r-biocgenerics - r-delayedmatrixstats - r-dplyr - r-ggplot2 - r-ggrepel - r-grr - r-htmlwidgets - r-igraph - r-irlba - r-leidenbase - r-limma - r-lmtest - r-mass - r-matrix - r-matrix-utils - r-pbapply - r-pbmcapply - r-pheatmap - r-plotly - r-pryr - r-proxy - r-pscl - r-purrr - r-rann - r-rcpp - r-rcppparallel - r-reshape2 - r-reticulate - r-rhpcblasctl - r-rsample - r-rtsne - r-shiny - r-slam - r-spdep - r-speedglm - r-stringr - r-singlecellexperiment - r-tibble - r-tidyr - r-uwot - r-viridis)) - (home-page "https://github.com/cole-trapnell-lab/monocle3") - (synopsis "Analysis toolkit for single-cell RNA-Seq data") - (description - "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") - (license license:expat))) + (let ((commit "98402ed0c10cac020524bebbb9300614a799f6d1") + (revision "1")) + (package + (name "r-monocle3") + (version (git-version "1.3.7" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/monocle3") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1qs4qcdz9hcq966qcr7xvkpx3ri8g1n5psfwik09m7ngzpdd1r5q")))) + (properties `((upstream-name . "monocle3"))) + (build-system r-build-system) + ;; FIXME Tests are apparently broken. 30 of them fail with accuracy + ;; errors. + (arguments (list #:tests? #false)) + (propagated-inputs + (list r-assertthat + r-batchelor + r-biobase + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-digest + r-dplyr + r-future + r-ggplot2 + r-ggrastr + r-ggrepel + r-grr + r-hdf5array + r-igraph + r-irlba + r-leidenbase + r-limma + r-lme4 + r-lmtest + r-mass + r-matrix + r-openssl + r-pbapply + r-pbmcapply + r-pheatmap + r-plotly + r-plyr + r-proxy + r-pscl + r-purrr + r-rann + r-rcolorbrewer + r-rcpp + r-rcppannoy + r-rcpphnsw + r-reshape2 + r-rhpcblasctl + r-rsample + r-rtsne + r-s4vectors + r-sf + r-shiny + r-singlecellexperiment + r-slam + r-spdep + r-speedglm + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-uwot + r-viridis)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/cole-trapnell-lab/monocle3") + (synopsis "Analysis toolkit for single-cell RNA-Seq data") + (description + "Monocle 3 performs clustering, differential expression and trajectory +analysis for single-cell expression experiments. It orders individual cells +according to progress through a biological process, without knowing ahead of +time which genes define progress through that process. Monocle 3 also +performs differential expression analysis, clustering, visualization, and +other useful tasks on single-cell expression data. It is designed to work +with RNA-Seq data, but could be used with other types as well.") + (license license:expat)))) (define-public r-noiseq (package (name "r-noiseq") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "1aph4phg58f4kpgavrxnn6dzh3lgms8sbjvip4f3gn8xs0p01mbz")))) + "0398hvwqr7cal7xnxbpv2dcbg3j5xhkv6n54h0niswrvd1d68fzy")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -15161,14 +16832,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "106hawmyln6xj9m2npibb4lkd8qvz60lwjabhn3cpx3908x88ryb")))) + "1l47w55b1qlj589c84g9jmxah8bf8gspw30bl9mpppyjh2nihg8p")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -15199,14 +16870,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1qvnc6cds3avxh1k4z47vb2fih7q8a5b9hccnyrpfks5c0sd6yi0")))) + "0cmjyxkszidsjzhs6rqw5m7afmy4gw2rvajrm5wagnisk73bvz6i")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light @@ -15215,6 +16886,7 @@ distributions.") r-class r-cluster r-compositions + r-delayedmatrixstats r-diptest r-edger r-fpc @@ -15229,9 +16901,10 @@ distributions.") r-rhdf5 r-ruvseq r-singlecellexperiment + r-sparsematrixstats r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description @@ -15243,29 +16916,37 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.72.0") + (version "2.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0rqyv95l8h3s68ywhv3r7hm7j1mbm8prql7p2rlvv4xg31yqmnpl")))) + "0lwi8cxlzgnd59bcn5mxkxijb292y857phafyskfs9k7951lxznl")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) + ;; Tests attempt to download data files. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biobase r-curl r-data-table r-dplyr + r-httr2 r-limma r-magrittr r-r-utils r-readr + r-rentrez + r-rvest + r-s4vectors + r-stringr + r-summarizedexperiment r-tidyr r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description @@ -15278,17 +16959,18 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.46.0") + (version "0.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "0l3n1plz5nvday0a1bm8173mikpfjbzrb1bp8yfvafy7lav4dsyv")))) + "1czvan67l4ib0xw76a9qgcwa0x2vswv752nrslj9k9mhdav6syms")))) (build-system r-build-system) (propagated-inputs (list r-base64)) + (native-inputs (list r-biocstyle r-illuminadatatestfiles r-runit)) (home-page "https://github.com/HenrikBengtsson/illuminaio/") (synopsis "Parse Illumina microarray output files") (description @@ -15299,14 +16981,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0j4nhdq82dzr19x5w4w4l97clra0z1kk6n24x56hrrj0xlm2cgnm")))) + "0d9yy4mgljgwfv1p57zqwxp7csvmbqzfp46kay0rfmrdad3qzrq7")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) @@ -15323,15 +17005,26 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "08b5d0grmpk5pryffdh6gdafhp1brana353q2kmwhz7x55aq3w68")))) + "185kxkx7lcnylfwp6c9hnnxarwa3rrwb1q45c5z6hl3wj7d74154")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This test attempts to download a data file. + (delete-file "tests/testthat/test_annotation.R") + ;; This file attempts to run the testthat tests, which we just + ;; deleted. + (delete-file "tests/test-all.R")))))) (propagated-inputs (list r-annotationdbi r-biocgenerics @@ -15346,6 +17039,11 @@ Bayes Analyses of Microarrays} (EBAM).") r-locfit r-matrixstats r-s4vectors)) + (native-inputs + (list r-doparallel + r-runit + r-testthat + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://github.com/ririzarr/bumphunter") (synopsis "Find bumps in genomic data") (description @@ -15357,17 +17055,17 @@ studies.") (define-public r-bumpymatrix (package (name "r-bumpymatrix") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BumpyMatrix" version)) (sha256 (base32 - "1f8xa184x6l363psbqn0a5yh16ghm2mciv726aii58bkln5qwkmb")))) + "1ffg36b35li50nx1gs0knjl32k0jlqyhcw6j7zqw651apfknvd4i")))) (properties `((upstream-name . "BumpyMatrix"))) (build-system r-build-system) (propagated-inputs (list r-iranges r-matrix r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/BumpyMatrix") (synopsis "Bumpy matrix of non-scalar objects") (description @@ -15383,13 +17081,13 @@ data in a format that is compatible with two-dimensional containers like the (define-public r-mia (package (name "r-mia") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mia" version)) (sha256 (base32 - "1wn2lb7hn4zqqcs2jwavpsbk5kw8d78kxg2yv4jjpikpdz7haa2i")))) + "1qf7dd9s66xmxsfv422cikrimyqiaqz71qc6yav119a9mbp8arpd")))) (properties `((upstream-name . "mia"))) (build-system r-build-system) (propagated-inputs @@ -15407,7 +17105,9 @@ data in a format that is compatible with two-dimensional containers like the r-iranges r-mass r-matrixgenerics + r-mediation r-multiassayexperiment + r-rbiom r-rlang r-s4vectors r-scater @@ -15418,7 +17118,7 @@ data in a format that is compatible with two-dimensional containers like the r-tidyr r-treesummarizedexperiment r-vegan)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/microbiome/mia") (synopsis "Microbiome analysis") (description @@ -15433,13 +17133,13 @@ summarization.") (define-public r-microbiome (package (name "r-microbiome") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "microbiome" version)) (sha256 (base32 - "1azxfydcrxi46j6lykspzchwcj0dpghjia7vfb2bppz9gh8nvk37")))) + "1q78d71gpczgphv9adh8lz6lx1q0wbiv4pl59aqz6cvagx0kcza6")))) (properties `((upstream-name . "microbiome"))) (build-system r-build-system) (propagated-inputs @@ -15454,7 +17154,7 @@ summarization.") r-tibble r-tidyr r-vegan)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://microbiome.github.io/microbiome/") (synopsis "Tools for microbiome analysis") (description @@ -15503,13 +17203,13 @@ experiments.") (define-public r-milor (package (name "r-milor") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "1cb5iw90h6raflgmypd2wc8y4mbsv9g8alshh30k1kjm8vlsw92y")))) + "1x7p6zjbif8wc4z8wqc472z69j3wbrbqbfq9sldj7v6cgfcflifd")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs @@ -15533,16 +17233,24 @@ experiments.") r-matrixstats r-numderiv r-patchwork + r-pracma r-rcolorbrewer r-rcpp r-rcpparmadillo + r-rcppeigen + r-rcppml r-s4vectors r-singlecellexperiment r-stringr r-summarizedexperiment r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr + r-mass + r-mvtnorm + r-scater + r-scran + r-testthat)) (home-page "https://marionilab.github.io/miloR") (synopsis "Differential neighbourhood abundance testing on a graph") (description @@ -15555,15 +17263,17 @@ model.") (define-public r-minfi (package (name "r-minfi") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "1hk44wddcygh4j7jmj1b0p40hf5qdy1m78x14j19h7z9aq4azdij")))) + "1n63pzyn153w24l6ydblah046dqv6fpcz4wi25j14myk12kwx1x0")))) (build-system r-build-system) + ;; Tests require r-minfidata, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-beanplot r-biobase @@ -15595,7 +17305,7 @@ model.") r-siggenes r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description @@ -15606,13 +17316,13 @@ methylation arrays.") (define-public r-missmethyl (package (name "r-missmethyl") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "missMethyl" version)) (sha256 (base32 - "0fnqa7v6lgld4pdqnvgdzly73aj4a4cn8sgszicxsyn1damxsjiw")))) + "1q149myhwhxnrnk5s9r3yx6dchzm70kkika4k12vm5plaxv29di9")))) (properties `((upstream-name . "missMethyl"))) (build-system r-build-system) (propagated-inputs @@ -15626,6 +17336,8 @@ methylation arrays.") r-illuminahumanmethylation450kmanifest r-illuminahumanmethylationepicanno-ilm10b4-hg19 r-illuminahumanmethylationepicmanifest + r-illuminahumanmethylationepicv2anno-20a1-hg38 + r-illuminahumanmethylationepicv2manifest r-iranges r-limma r-methylumi @@ -15656,14 +17368,14 @@ into account multi-gene associated probes.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1ms3w43yvy810mr6dml9hqp3kw5jlpr9153kd62gvhjsgikaj3ja")))) + "15lc81qdvjk6mr74h59gr2bxq9alj1wjady2h0j7rhq0p7rim754")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -15703,23 +17415,31 @@ and Infinium HD arrays are also included.") (define-public r-lefser (package (name "r-lefser") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lefser" version)) (sha256 (base32 - "1qi4q3vijys4q1gfnflvvz8ws3j6f65rpprpgmrkqgiwfn7dvi6g")))) - (properties `((upstream-name . "lefser"))) + "1kq64150kjcqfqrnj1vpn83345xpvnxw3kddg5c36hwww3bh2mpj")))) + (properties + `((upstream-name . "lefser") + (updater-extra-native-inputs . ("r-mia")))) (build-system r-build-system) (propagated-inputs (list r-coin r-dplyr + r-forcats r-ggplot2 + r-ggtree r-mass r-s4vectors - r-summarizedexperiment)) - (native-inputs (list r-knitr)) + r-stringr + r-summarizedexperiment + r-testthat + r-tibble + r-tidyr)) + (native-inputs (list r-knitr r-mia r-withr)) (home-page "https://github.com/waldronlab/lefser") (synopsis "LEfSE method for microbiome biomarker discovery") (description @@ -15732,14 +17452,14 @@ to find biomarkers of groups and sub-groups.") (define-public r-lumi (package (name "r-lumi") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "04r7dw00yvjrxs0h6mwh79lwp55f5v8s4pgmzcy2fnpb2cdslpzy")))) + "14bmwkbv9zppwql085g01m1q2wncmnb4q8gid5mwgdpr2gnkfwib")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -15771,14 +17491,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1la6fwaap7957rrb4cs6w48kjz4hqrw3h39lpps419d4cbnsp5jz")))) + "03prx6qzkk5cdr83x4i3m2irjsm9ay31bz581ms0ji27y5l7c0wh")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -15801,7 +17521,7 @@ especially Illumina Infinium methylation microarrays.") r-vegan r-zoo)) (native-inputs - (list r-knitr)) + (list r-knitr r-matrixstats r-moments r-testthat)) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description @@ -15832,14 +17552,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1ihski4akl70v6kq03di6w1pz63dx6rxgmyjkm0dv0nhgkmrza22")))) + "1jb540h8klzxywm9dndijx04fnvk0gih9kxi351l24fwk8vppiqb")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -15857,7 +17577,7 @@ evaluation of DEG analysis methods.") r-tidyr r-xvector)) (native-inputs - (list r-knitr)) + (list r-knitr r-minionsummarydata r-testthat)) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description @@ -15885,6 +17605,7 @@ surface of a flowcell.") (build-system r-build-system) (propagated-inputs (list r-multcomp r-multtest r-mvtnorm r-plotrix)) + (native-inputs (list r-testthat)) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description @@ -15928,13 +17649,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "1kgvvvwvj3dgb2wik3y8j44ynda94bi05vvmiwlayrypqprwi1c1")))) + "1wfq76g6mqf0gkqi9jxqb5va8v59k4ivbdm8d3plmpb6rd23n2ha")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -15958,7 +17679,7 @@ published results; and a routine for graphical display.") r-trajectoryutils r-viridis)) (native-inputs - (list r-knitr)) + (list r-delayedmatrixstats r-dplyr r-knitr r-testthat)) (home-page "https://statomics.github.io/tradeSeq/index.html") (synopsis "Trajectory-based differential expression analysis") (description @@ -15984,8 +17705,11 @@ performs inference on the parameters of the GAM.") (base32 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) + ;; Vignettes need deprecated package RangedData. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-biocgenerics r-iranges r-yaml)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description @@ -15997,14 +17721,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1idil9vkd5risx9ahkagdacnj2g2a11gzsd7wmhg5gjmr77r53ww")))) + "1wv3xklgggn6ajjf7l068ybr1x38n6dv0kkkxna7d39y7q2dfqxc")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -16022,6 +17746,7 @@ peak definition in combination with known profile characteristics.") r-rtracklayer r-s4vectors r-variantannotation)) + (native-inputs (list r-lungcancerlines r-runit)) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description @@ -16037,14 +17762,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "1pc63hk0smcflq4903hvs4pp8r0kzlx08j0m1kxlh14cxwppamyb")))) + "1kfm07dcs4gvkr1ry57q8r564v2b73vd67ysy83riz9qvan5r63b")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -16062,14 +17787,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.30.2") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "009rh51mndpkqw9vmr836ll2zsmsb4wlrjhvda5qiggznlhixrcv")))) + "0ql5mxaks11dpkykggylnpi2jymh467w1zqi6s6bp1gb4h399jly")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -16077,13 +17802,12 @@ information about samples and features can be added to the plot.") r-dbi r-digest r-go-db - r-httr2 r-r-utils r-rcpp r-rlang r-yulab-utils)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description @@ -16097,14 +17821,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1pg9p6982901k08iqpk0cdb9hii3k7bci9gq6an711r8a4iy3lmc")))) + "1y5gxm896la45f2psdc2792nw25a8mxd3b45i9kh68wni6d2drdr")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) @@ -16127,13 +17851,13 @@ the data set is suitable for such analysis.") (define-public r-anota2seq (package (name "r-anota2seq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota2seq" version)) (sha256 - (base32 "140k37wswl4w2136pz9y0z82sphzxmgzgk3cr400kkm39wjn7vxm")))) + (base32 "0lzpp2pxbpza1wijmj9cz9ia94pyc5b5fknw2njy0qv8rcwxjwhh")))) (properties `((upstream-name . "anota2seq"))) (build-system r-build-system) (propagated-inputs @@ -16163,13 +17887,13 @@ that protein levels remain constant despite fluctuating total mRNA levels.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "1gb15zrv44yn65wns7dk24rp54qv7wafqxgk1q8jnbkq9lp5wj2y")))) + (base32 "0llrp1q8py5rz9zd497yv3l0ranhdn6jmrwxam2byih2j35w8gbx")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs @@ -16181,7 +17905,7 @@ that protein levels remain constant despite fluctuating total mRNA levels.") r-rtracklayer r-summarizedexperiment r-variantannotation)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/fcScan") (synopsis "Detect clusters of coordinates with user defined options") (description @@ -16196,14 +17920,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0nnvqsyrj24h5y8qw8llk9f4jgy0v734k37kcksfcpja17frdyjy")))) + "05bvxdmyg4l99j2cb63mdsc5572i421kx7ax6ii2aig3299wsyxx")))) (build-system r-build-system) (propagated-inputs (list r-bh @@ -16216,7 +17940,7 @@ presence of additional sites within the allowed window size.") r-rcpp r-scales)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description @@ -16229,14 +17953,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.30.4") + (version "4.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "07pljijlyp4labxg4q3kf6wq4acw6axyyw57k1bws3hcf4m1d92x")))) + "1x0dnlbgx2wsiki7l7c8np7v8kh4m5f30yjnavfzg9pjy3j98myq")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -16246,9 +17970,10 @@ to multiple hypothesis correction.") r-ggplot2 r-gosemsim r-qvalue - r-reshape2)) + r-reshape2 + r-yulab-utils)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description @@ -16263,13 +17988,13 @@ data.") (define-public r-enrichedheatmap (package (name "r-enrichedheatmap") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnrichedHeatmap" version)) (sha256 (base32 - "0fmqz9xqs1108a5xxpsc63pplcc0i742r4zdk46p68my28ba2xfq")))) + "0qihf4ff9wwg2yfm5lgc8g59ni1spm3n2wjmvp2md83571cczm15")))) (properties `((upstream-name . "EnrichedHeatmap"))) (build-system r-build-system) (propagated-inputs (list r-circlize @@ -16280,7 +18005,7 @@ data.") r-locfit r-matrixstats r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jokergoo/EnrichedHeatmap") (synopsis "Enriched heatmaps") (description @@ -16295,14 +18020,14 @@ correspondance between different data sources.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.24.2") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "03p0a1vyaznk405xpkp57f22wg8x7lxiipjh101p7dq97rbzr4r7")))) + "1fbn0bihxgb45lx6pl9n0dz91plmbdlly6898aq5cd7r17c23nr2")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -16310,7 +18035,8 @@ correspondance between different data sources.") r-ggfun r-ggnewscale r-ggplot2 - r-ggraph + r-ggrepel + r-ggtangle r-ggtree r-gosemsim r-igraph @@ -16321,7 +18047,6 @@ correspondance between different data sources.") r-reshape2 r-rlang r-scatterpie - r-shadowtext r-yulab-utils)) (native-inputs (list r-knitr)) @@ -16363,21 +18088,20 @@ attempts to assess their statistical significance.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.12.6") + (version "4.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "185g4pp3q78c5kxz8gqk3pl0f2xnp8fqffwi5rqsvs026cq06biq")))) + "1dhp3jfmz9zfp9nldd38fjkqvxq4piy2zpndrqmx1p53hcpss34l")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-dose - r-downloader r-dplyr r-enrichplot r-go-db @@ -16392,7 +18116,7 @@ attempts to assess their statistical significance.") r-tidyr r-yulab-utils)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description @@ -16403,16 +18127,16 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "0pi6qnchh89fhfr50fk4hrrkz1r8gfwjcd7254pgiaxcazv2380a")))) + "1csj6xn5kldfrrzl5qhd5dh59c0inmabx5pbbjq0zb2rad5scqj9")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (propagated-inputs (list r-ape r-biocgenerics @@ -16448,14 +18172,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.84.0") + (version "1.86.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1m8clkb5rznzv2fwrl59csq8v0ibqwdm4fphq10b8pmyvj880qpn")))) + "1r00hcisp4i2q7nki9rkp753ms3g7biw9h9hxfwajfjqlwpb3l5y")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -16480,7 +18204,7 @@ expression data sets.") r-shiny r-summarizedexperiment r-threejs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-golubesets r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") (description @@ -16492,14 +18216,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1298mn8yz4i0qqw1i8pd4ym5f65dmyb8wcmpyahzz11na4diybmj")))) + "0spsiywh2xxzi8xjg2gk08p4fpha01pc0x65z18gsps6lh1zj1gk")))) (build-system r-build-system) (arguments `(#:phases @@ -16524,14 +18248,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1jn2ikzijd282jl96i9hcvahkc6l2vsd79dxqiz7kwaqcp7hs5z9")))) + "0rc3aragscizy067qx46sc5w2d5cimdizkmcy41y771aj1kbpygh")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -16548,14 +18272,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "15jcd66brvbjz0p3z2b43ac5k81s3vmcbkwmga0f7f5v53fp8qvw")))) + "0h6i6nxfq2nnla8559bjinydaywwc8lzg0xs8z2adj4cr52r6h74")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -16578,14 +18302,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1yphs36pk2y4qajq24y443yzb2f55b08nl81ylpf65mvxlxd23w2")))) + "108ns2ln2j5bkaqmah0w8132b2p995wrcd4a98a1vnsgs806mwfp")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -16602,14 +18326,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "08zlg74qryqm238mld876v15a6c71brkz2y1gnbj0rnl1l9f9rbh")))) + "11zpq6zk67m72qx09ng6g4h32206f6lzldndirwxzqbv0ix9yy1v")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -16626,14 +18350,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "19vapjmyd3ly3s2gqa2xfg99gyc6n6lv3c6rpi0ch4hzb7wiinvm")))) + "1x62125rinav1g3s549f4s59z3ddcmzznnghlh8w54sabnz3i45d")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -16657,14 +18381,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1wzqpvz49wkbvqij48c3l6vqfvflgic8gzvjdigb1c6mr96l6vgg")))) + "0izl2b306lj9768p1lxi02sj6sbih5isa0f2k6g8igjq7z08mk8c")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -16678,14 +18402,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0aj3kh4c8zk60n6yyh2jblbrvv77071r96m0mrcslqm71dwg9402")))) + "1d52aiix3pixhcr6pjmz48p4wkcik4cwpbq4fhngv48y1sgd5d8i")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -16710,7 +18434,7 @@ Affymetrix arrays.") r-vegan r-venndiagram)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description @@ -16726,19 +18450,19 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "09lvjb0fa70kcl7mkp4agxv6jcm2ncmnrffav6zmz038imhmvdgm")))) + "1ihhxnz5b12r6mh9j4k9nzwxaiw9m3mgc740y4j6xz67csi0xih0")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/bacon/") (synopsis "Controlling bias and inflation in association studies") (description @@ -16751,14 +18475,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "1d1vfnxj1p4y1074ybmkxv4x3v0i3sn5w3k4bddzlrqbzyb9kkna")))) + "0lcsw14n3acxljx6zsrfh0hp3s6y0638jzzrh2f2p0jc9mj29b8y")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -16805,12 +18529,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "1m8y76gg80625xz9g9101mfq19glk37p792yzz46807f7g6m8zbh")))) + (base32 "0bgq927ch7b79sypr5fxgw6d2y5q0srny2k2ysxsyhcbagpl42b8")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -16822,7 +18546,7 @@ distributions, modules and filter motifs.") r-s4vectors r-splitstackshape)) (native-inputs - (list r-formatr r-knitr r-markdown r-rmarkdown)) + (list r-formatr r-knitr r-markdown r-rmarkdown r-runit r-seqlogo)) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -16832,19 +18556,24 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "1mxs83l8yrbcx353h0wpc0lczn1jc0y5vg59y9g9dabk41csib47")))) + (base32 "0308wqrcjzdfm38p9lqphz5h82k2zdzknvhviqzrvcqinzqjqy26")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs - (list r-biocgenerics + (list r-biocfilecache + r-biocgenerics r-biocparallel + r-biomart r-biostrings r-bsgenome + r-bsicons + r-bslib + r-dt r-genomeinfodb r-genomicranges r-gviz @@ -16855,10 +18584,12 @@ frequency matrices from nine public sources, for multiple organisms.") r-pwalign r-rtracklayer r-s4vectors + r-shiny r-stringr r-summarizedexperiment r-tfmpvalue - r-variantannotation)) + r-variantannotation + r-vroom)) (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/motifbreakR/") @@ -16883,14 +18614,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "15v4z1a0kg4ic411aprzc9b7i2l6c456sfj3jaxy95anw3j3iskj")) + "0wkv0gjvk7p491c4zsg1hh61r3lhmjnif6nd2s63xwqm2qw6a4nx")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "motifStack"))) @@ -16914,7 +18645,7 @@ Bioconductor.") r-tfbstools r-xml)) (native-inputs - (list esbuild r-knitr + (list esbuild r-knitr r-runit (origin (method url-fetch) (uri "https://web.archive.org/web/20230428092426id_/\ @@ -16935,14 +18666,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "11sabicr2jm1cc9rdjr6vjqhf0gd9d7k04qlfhcdssvh02f957ia")))) + "1b9fzkch7xqn0f56psq0vnhq46ysl6nnd7f2hf2hxsm0w1z6q1z6")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -16962,7 +18693,7 @@ type and symbol colors.") r-s4vectors r-xml)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description @@ -16983,6 +18714,8 @@ position-specific scores within R and Bioconductor.") (base32 "1r7z3n6wyrd2cclj5b7sg15wpmjdh9k5b1hjlw7jjx8j384l7l1h")))) (properties `((upstream-name . "GenomicState"))) (build-system r-build-system) + ;; Tests require Internet access. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-annotationhub r-bumphunter @@ -16992,7 +18725,7 @@ position-specific scores within R and Bioconductor.") r-iranges r-org-hs-eg-db r-rtracklayer)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/LieberInstitute/GenomicState") (synopsis "Build and access GenomicState objects") (description @@ -17004,14 +18737,14 @@ these files at JHPCE.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0licdpzhh6xlma0hnvs4rr4bjr5q4q3g18kipf0is47zj4l91smy")))) + "128ka9fzj8zy6mlccszi5xnq25ivhpgq08q9jsiazm65kzxpvqfb")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -17035,7 +18768,7 @@ these files at JHPCE.") r-rtracklayer r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ATACseqQC/") (synopsis "ATAC-seq quality control") (description @@ -17052,14 +18785,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1g3nppcmyj81ia3v9zvsr8jplk8kmvssspvxd94zxh6yb3wrrc6v")))) + "0s6dmfv2cd88crhmq1i5sp7r37l1zabdxwdspydz9mh3008mqrqp")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -17071,7 +18804,7 @@ footprints.") r-rcpp r-vioplot)) (native-inputs - (list r-knitr)) + (list r-homo-sapiens r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/GOfuncR/") (synopsis "Gene ontology enrichment using FUNC") (description @@ -17119,7 +18852,7 @@ annotations and ontologies.") r-gtools r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description @@ -17157,14 +18890,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "1hwawrp0pbrm9xf7fn65nj0q4s49qlnmxfjlmrv5fykyn3i1lhpq")))) + "03hqhq6xyaf24ryrnf9q3x00m8600kxhinzag8a9cvw1x0h2d1pz")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -17182,14 +18915,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0mbmw450gdlr46ggvhrgimkbir3lg5dnqsfadn7yyrn7wkcr302f")))) + "1grjrbq15xd05m819j7804v3hzrjnmqj7jmdypc2wn53jxnbpqf5")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -17214,7 +18947,7 @@ text files).") r-summarizedexperiment r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description @@ -17225,14 +18958,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "009ha82393giapvmfw2mi8pmi88f61mr69qj64y5vphcr1smvcl0")))) + "1n5xb6qymfywglnnh1klxlqzhry78kwn8zlpvz7z06w6ixfc9q80")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -17246,7 +18979,7 @@ investigation using RNA-seq data.") r-r-utils r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description @@ -17265,14 +18998,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.46.0") + (version "4.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0qaafn9l9lwrj0yph74g39pghjpg009qz7by64frxg1q0j7ksd2w")))) + "16p3bzs13ihfx36fav3y1dxfryhyj00wvcwqc6mzx5ln2a2jpdbv")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -17304,14 +19037,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "0l9wqijwlq1gwybj2fy6jwgq6ja1mvx8yfdv174g5mjflx8nmc06")))) + "1rdqx69x4qqq6lnsk54rha8am51likxvlyqj4lk7rx5gg2390d5q")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -17324,7 +19057,7 @@ visualization with image data.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description @@ -17337,19 +19070,19 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "1qlsjpjxcw96qhrqjlbbinpry9yagn50jc3dnz459dbfvnywr82q")))) + "1cf98aric80hz6jqriyk8m1cr4d9pxsjv7pixss2qsp797qvf87z")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description @@ -17363,14 +19096,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0yvn2famnyxkxnw4r1vr0vma6ym9kb343vqgaqkvcp3zpm1fi0p8")))) + "0qvlfcsb4wwk1h0gi0gira7vknpd6jkyzil9z05mbgip9cyn543n")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -17389,7 +19122,7 @@ genomic categories and to add self-defined graphics in the plot.") r-s4vectors r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description @@ -17402,14 +19135,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "0908hyji07br1i1zms21a99m3mvi707xj8zbd1w64gzackghabhl")))) + "1yc8j06v4ap5zvzvd40rfzc6fd9a295m7mwskis76qs4nhz29hz5")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -17437,7 +19170,7 @@ decomposition algorithms.") r-somaticsignatures r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description @@ -17451,14 +19184,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.76.0") + (version "2.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "01b9b4v19yh42552awl21yyx9vhf9yh9r3l8849x4zwjpnf6anp3")))) + "0v397nmmm6zy5pipzgz81fhkygg4hz173dvm28cm4813pjrq7gsa")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -17533,14 +19266,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "0b8afvnczkhmbdg5zna2h5v42zdyvk1zybn9cwcbw22rijiysq99")))) + "0hkrpg2x7w8kgw8hblw0q178h5kb09yir1rg4jji1irbl4g1drck")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17551,7 +19284,7 @@ chips with the MAQC reference datasets.") r-minfi r-rcolorbrewer)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description @@ -17566,14 +19299,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "1r0dj65i8xg1yb6x7ggb3s40hvzbh596k2g9bxblsbl18z867ydp")))) + "0iy130bkx549jn9ki7zgmxw78md9l6rr98rwmv9jzv2a09bddl2c")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17588,7 +19321,7 @@ groups.") r-rcolorbrewer r-readr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description @@ -17603,14 +19336,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "06d1w5kknm2mb6v6glmyd97n1a33529kgqkkyfbk277ikn45hi9f")))) + "0mvb1vgjy6d3q9wh5a7a0s4cmy3hx15fl9fvh74yv5ywggp99n82")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -17621,6 +19354,7 @@ large RNA-seq experiments.") r-rtracklayer r-s4vectors r-summarizedexperiment)) + (native-inputs (list r-rnaseqdata-hnrnpc-bam-chr14 r-testthat)) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description @@ -17653,7 +19387,7 @@ sites and alignments obtained from standard RNA-seq experiments.") r-pracma r-roar)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description @@ -17671,19 +19405,19 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0ckvnah0ck5z6calgrwk0k3y1nxpcyn41y84kz5bypzr77x6ssj2")))) + "0nxfadb19k40y7l20sw9casq1cabgbfz64jqv9yv911mr6l6m6fs")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description @@ -17695,21 +19429,26 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "4.2.3") + (version "4.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "10b3jj7m278df0s83icbl95rbp5m7y0avhsjzfy0mkgyvm13y5ls")))) + "1i9xiilrwvnzkdbzrdnbsw0sbwplfaklbsk3wz8kzv87ivipybh5")))) + (properties + '((upstream-name . "xcms") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-faahko")))) (build-system r-build-system) + ;; Tests require faahKO, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel r-iranges - r-jsonlite r-lattice r-massspecwavelet r-metabocoreutils @@ -17725,7 +19464,7 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") r-spectra r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-msdata r-testthat)) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description @@ -17738,13 +19477,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "1mvr5bpsng87yl1bhd22h45830vw3sla1ysnr29px13if2q5ylmy")))) + "0vd90v88k1p5ljbdyd0s2qhsr4b2ja16w610ab41rxwpf62vmxgz")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration @@ -17766,7 +19505,7 @@ data for high-throughput, untargeted analyte profiling.") r-rlang r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/AnaGalhoz37/wppi") (synopsis "Weighting protein-protein interactions") (description @@ -17779,14 +19518,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1nwbqagpcs38c66r1arbby76if6pafa4snd6zbp18y71jj8rgvl7")))) + "151a4fnrdghayaj6fhkfxl2s1rjc1ph0gbf9hfkz4s5mxj92fc5a")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -17803,14 +19542,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1px7rgvaj6kks6fp7yqsqjwy4knlzgllzxsiimv8nikmbd57dmi0")))) + "1p0x3zrp5hvrfh7cyxdxgniij3yjawrsm1pnz0sw75ps00kw3kpn")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -17824,7 +19563,7 @@ that arising from 16s metagenomic surveys.") r-rtracklayer r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description @@ -17837,14 +19576,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "0knszrfapndnjzv5948qbfsjamlf7g04yry7yx294l8iwvwip6qv")))) + "0mi8xnwwlcdh3vj58fg69xbqv12k8xp5jbbd2kkrhcpcvkw0lnxb")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -17858,14 +19597,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1ws4w2kf514adk50sjadgasm7z1xvklcb8s243m12fvlg63dia9i")))) + "0wvkbma50q6ibckhsimarc0qb0rr65ph85amxq2lihvc9w69b7p8")))) (build-system r-build-system) (inputs (list netpbm perl)) @@ -17890,14 +19629,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "07zlvzfs1c4gcj9hwgqbjhgbrffi301620chrf5lvzly4v7hafwi")))) + "0z0414h470674g0w6y11i1mc06vrc075zdcyjjhsj1i8npwqym60")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -17908,7 +19647,7 @@ Currently only Affymetrix oligonucleotide analysis is supported.") r-softimpute r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/zinbwave") (synopsis "Zero-inflated negative binomial model for RNA-seq data") (description "This package implements a general and flexible zero-inflated @@ -17923,14 +19662,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1pgmw41xdq9gd2shc6kawgxz9sw1ydlgs0p35k99k2v50f86r2wy")))) + "1hhlx7xqjlnm90j8hk5qypk225n4w38qsn2v4vdaar96z6lm2rnq")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -17948,14 +19687,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1spwpbx1jjfjcxbwjkl64ccp9k8xs6lm828546qddsgp20y3bhgp")))) + "1jk0h0ms984bc5k36vb9z9mldpa70yibxl5ppf5i2q09py7higa7")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -17963,7 +19702,7 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (inputs (list samtools zlib)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description @@ -17975,14 +19714,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "1f5y1sza9vm7wqd4mp5g7sypc9kbf9zpl015rbl41wz4y3ai21sb")))) + "0ysxjady2cc3rijc3m2izd48zwm039scbk1h51z0926hyqg56h9c")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17994,7 +19733,7 @@ rapid adapter trimming, identification, and read merging.") r-reshape2 r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description @@ -18007,14 +19746,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "0wg799c5pzw9g0dbkaa5j4jyccvixqbc8x3xnwk3cgi1dsbhpk34")))) + "0v6b86gaqszbbp8dx9i8bkz95lxkb4ci20w1l596b3vzqs2a8fb2")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -18030,16 +19769,18 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0jv6hni5x91ssvz4ilhi3y6lylrw4w3xfk8ljmq6gjvyl886sw9f")))) + "08j0589rwylirna6r4bwk5vb965fp4zpj0msk0mlhppngqzlc2kc")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) + ;; Tests require internet access. + (arguments (list #:tests? #false)) (propagated-inputs (list r-curl r-dbi @@ -18062,17 +19803,17 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "01rf4w2p1qw4hk9shsdaffyz9g91vffcn4qi1dllsrn3m8pyd1gm")))) + "0ir2xshq4qmzyli9v14cmlk262px47ng5gd23r4sf6p065xnws6m")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-biocgenerics r-runit)) (home-page "https://bioconductor.org/packages/iClusterPlus/") (synopsis "Integrative clustering of multi-type genomic data") (description @@ -18092,14 +19833,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1in3qani4xh5m5zpbny1nbsvh60ahs36bas8hplkdpd8hnhfla56")))) + "0cbdg469796ij1n8l42mp1c30y2r28j7as6q7add38rpfrmj57b7")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments @@ -18116,7 +19857,7 @@ Gaussian distributions.") (setenv "POPCNT_CAPABILITY" "0"))))))) (inputs (list zlib)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description @@ -18128,16 +19869,24 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "1i3dg3fn648mzy49m15vbzr3wfnk91xyph5j4sc7ss978l25h17n")))) + "1xchrzd384wzm81vzrcixyzn3mgnd343cp544yvfzfn2vxr4y1ij")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This test attempts to download a data file. + (delete-file "inst/unitTests/test_predictVariantEffects.R")))))) (propagated-inputs (list r-annotationdbi r-biocgenerics @@ -18154,7 +19903,7 @@ alignment tool.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-runit)) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description @@ -18171,14 +19920,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0a7k9p08gq537275r7dfzh34ycxx8h4fmac74jimwhsa420793r5")))) + "1gmkr0k6qlp3cp4pkankasv098rf7bjrw5bm905w5m4mzw0r1sai")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -18196,7 +19945,7 @@ interpretation.") (propagated-inputs (list r-genomicranges r-sgseq r-txdbmaker)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description @@ -18209,15 +19958,17 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "116qnp7d7z4a56fv6n55yzrdlmma9gwrw234nmy8iapkn5ms3xky")))) - (properties `((upstream-name . "QuasR"))) + "14c923hhk9pn2a6kslcw5ai5xn50bba43fp9b5p9viaqikgr2nby")))) + (properties + `((upstream-name . "QuasR") + (updater-extra-native-inputs . ("r-rhisat2")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -18239,7 +19990,7 @@ index.") r-shortread r-txdbmaker)) (native-inputs - (list r-knitr)) + (list r-genomicalignments r-knitr r-rhisat2 r-testthat)) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description @@ -18252,14 +20003,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "0szd5ygcvpaiwqss8galxzxpslpfh93rk42s865v0qpv0s9v9x0l")))) + "061nrck7d8499bc92m24fv7zyyb98lwjrqrbpmab0pa79vh2q1zz")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -18282,7 +20033,7 @@ quantification of genomic regions of interest.") r-shiny r-shortread)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description @@ -18295,18 +20046,19 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.36.0") + (version "3.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1l3hkq6n7i9j82aym4ngwablj8jqb70a7y6skx0rjkflya6wbim7")))) + "0503vd2alhpda2brqgg0cqw6w9bad3yz92gsm4fbmyf1lklwlhg8")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-rtsne r-slam)) + (native-inputs (list r-biocgenerics r-runit)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description @@ -18348,14 +20100,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1y1j5svi52cvixjsn13122kvd0z0c7zfki3p6rr8wjd5w7riiyqw")))) + "048wnzw5qkfr0fhcz0i031zxz7xkvwyc451a1xbllkqpb9jsvi50")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -18370,7 +20122,7 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description @@ -18385,14 +20137,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "0cdkwzrbr6h1dfi3qdh629hi2jlm1hxgq4dvx4z3vc2r6w0c6m11")))) + "0f1qbpndil49d9friavzyhbfrp5176w2hrx79wp6b94afggil26h")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -18402,7 +20154,7 @@ packages.") r-plotly r-summarizedexperiment)) (native-inputs - (list r-knitr)) ; for vignettes + (list r-knitr r-testthat)) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description @@ -18427,14 +20179,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1c56s8lr5cdx27v0rdi4l4h680x6ga9wazf4dj1xkqyliqz65ps5")))) + "0d2prfx2w3kfja5gzp88q15cnhaswx2kg30l1zcb0bnsvzfblr8k")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -18445,7 +20197,7 @@ coefficients).") r-ropls r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description @@ -18462,15 +20214,17 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "11cc3nknbckm0v5r7dzgqzw0137w4c08ab10s9svb1y02z45a0qz")))) + "11j633mhm4b0ndl6mbqqwgz7rsggb7gzr3yhvamrnvag7l4wzvss")))) (build-system r-build-system) + ;; 5 tests need internet access. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-annotationhub @@ -18486,7 +20240,7 @@ datasets.") r-rtracklayer r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description @@ -18503,14 +20257,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0nd5b1k0dsxpf93wqx01fgbvk40jcfs7b7w692bsx620lm42ipfg")))) + "1n7pvx30sm6fxmydn33v2cr1nlrbdd8kqzg6pw9l78zaydqbl8r3")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -18529,13 +20283,13 @@ and to both short and long sequence reads.") (define-public r-flames (package (name "r-flames") - (version "1.10.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "FLAMES" version)) (sha256 - (base32 "1fcz0v1vy0q5zmdpawlk4a7fbqd01954p0jby9nbzgbk85hl16mi")))) + (base32 "0fhgis2grzzpzarlza4kqw8ysanlsw410wykjjakk35pyx275j8m")))) (properties `((upstream-name . "FLAMES"))) (build-system r-build-system) (arguments @@ -18548,10 +20302,13 @@ and to both short and long sequence reads.") ;; being run despite the check failing. (substitute* "src/Makevars" ((" & ") " && "))))))) + (inputs + (list minimap2 samtools zlib)) (propagated-inputs (list r-bambu r-basilisk r-biocgenerics + r-biocparallel r-biostrings r-circlize r-complexheatmap @@ -18571,18 +20328,21 @@ and to both short and long sequence reads.") r-jsonlite r-magrittr r-matrix - r-multiassayexperiment + r-matrixgenerics r-rcolorbrewer r-rcpp + r-readr r-reticulate r-rhtslib r-rsamtools r-rtracklayer r-s4vectors r-scater + r-scatterpie r-scran r-scuttle r-singlecellexperiment + r-spatialexperiment r-stringr r-summarizedexperiment r-testthat @@ -18590,9 +20350,8 @@ and to both short and long sequence reads.") r-tidyr r-tidyselect r-txdbmaker - r-withr - r-zlibbioc)) - (native-inputs (list r-knitr)) + r-withr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/OliverVoogd/FLAMES") (synopsis "Full Length Analysis of Mutations and Splicing in long read RNA-seq data") @@ -18606,13 +20365,13 @@ for manual execution.") (define-public r-flowai (package (name "r-flowai") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowAI" version)) (sha256 (base32 - "1siqza92iak5lz38hbfznqndrmq995ihp6sbam0n2d3mj8vwv9qa")))) + "1g2bjfdrmglxb2b3h3j2d37nq7k4hy2ff3qp5jy1arjrblq45qfm")))) (properties `((upstream-name . "flowAI"))) (build-system r-build-system) (propagated-inputs @@ -18625,7 +20384,7 @@ for manual execution.") r-reshape2 r-rmarkdown r-scales)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/flowAI") (synopsis "Automatic and interactive quality control for flow cytometry data") @@ -18672,14 +20431,14 @@ the quality control enables the detection and removal of anomalies.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "0y91kz1n3byadk505432cnlj9dfiw521fgb460d6dmly9s0d9yif")))) + "06lrjjl7h9d3xyi1j9ciikrqjmpqxvw2d0z1yifwd1lwx6b6zsgb")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -18726,7 +20485,7 @@ cluster count and membership by stability evidence in unsupervised analysis.") r-sva r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/biosurf/cyCombine") (synopsis "Integration of single-cell cytometry datasets") (description @@ -18741,17 +20500,17 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0nrj892jihi4fv58si3il42s0vyz3gm4gmb65kidkky63gmsy6iq")))) + "1fbsdpm2v9mzb4n5r5lf9z6v3gzmxd0x5dqs863p0ll1b8a6w7qv")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) - (inputs (list openblas protobuf zlib)) + (inputs (list openblas zlib)) (native-inputs (list r-knitr)) (propagated-inputs @@ -18766,16 +20525,18 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "1zq3qypmzk9ld48r50fmygfdqwwyykii8l0l6gh5bdrdan760bfn")))) + "0zbxlwij9nc2fpsx5hg2q9inn1g5c0i34bmvbn6n56y3i0vzm8xj")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) + ;; Tests need r-flowstats, which depends on this package + (arguments (list #:tests? #false)) (propagated-inputs (list r-bh r-biobase @@ -18787,7 +20548,7 @@ interact with gated cytometry data.") r-rprotobuflib r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -18798,14 +20559,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "0bkp3q71qj1r2bwfpfriflqklvcqpvh760as7sr489sb18y1xlms")))) + "1sgk1x1cm2srrdv2bn312lvj1pcc8r9gaqlvr1fnngp98dhw5pb1")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -18821,16 +20582,27 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1mbq3190nxlzhfb58i7s2f5f9fngda1icnihmyplagh64savlpcn")))) - (properties `((upstream-name . "ncdfFlow"))) + "16djrka94dhj041sd52ni9r5283fpnj5h5ljzzjqfik10fc9k5z5")))) + (properties + `((upstream-name . "ncdfFlow") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-flowstats")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Avoid dependency cycle. + (delete-file "tests/testthat/test_ncdfFlowSet_accessor.R")))))) (propagated-inputs (list r-bh r-biobase @@ -18840,7 +20612,7 @@ change point detection.") r-rhdf5lib r-zlibbioc)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description @@ -18851,15 +20623,19 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0z4cfpylj2y3jcljzg15fpjnrhrpzgw49kcprq5sg4cxr96ia2rm")))) - (properties `((upstream-name . "ggcyto"))) + "0a74lb36482djxfr77akyqqa7wnj9y3g4fkn8ain2gsbb3l6kcbk")))) + (properties + `((upstream-name . "ggcyto") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-flowstats")) + (updater-extra-native-inputs . ("r-flowworkspacedata")))) (build-system r-build-system) (propagated-inputs (list r-data-table @@ -18874,7 +20650,7 @@ manipulation of flow cytometry data.") r-rlang r-scales)) (native-inputs - (list r-knitr)) + (list r-flowworkspacedata r-knitr r-opencyto r-testthat r-vdiffr)) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description @@ -18888,16 +20664,22 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "1iz4skfs68jg2a59kfaxllf19mp9pk9mpfc2jh3vyas14c3l3zzj")))) - (properties `((upstream-name . "flowViz"))) + "1ymqx5zasrr5snmg71p58hk526yxpvs4d78df2hgxfah5w6vxd6w")))) + (properties + `((upstream-name . "flowViz") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-flowstats")))) (build-system r-build-system) + ;; There is only one test file and it depends on r-flowstats, which + ;; depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biobase r-flowcore @@ -18909,7 +20691,7 @@ statistics to the plot.") r-mass r-rcolorbrewer)) (native-inputs - (list r-knitr)) + (list r-knitr r-ncdfflow r-testthat)) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description @@ -18919,19 +20701,31 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.42.0") + (version "3.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "1zjjzn10nvbj7lhg9kvp8gr7m2m294pa3zdmajq65ffdynaaavnd")))) - (properties `((upstream-name . "flowClust"))) + "0li9vcgk82vn5wqzmz6hbn04vqa5l0mwsb6vyb537mkcg45dhcr3")))) + (properties + `((upstream-name . "flowClust") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-opencyto")))) (build-system r-build-system) (arguments - `(#:configure-flags - (list "--configure-args=--enable-bundled-gsl=no"))) + (list + #:configure-flags + '(list "--configure-args=--enable-bundled-gsl=no") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; "invalid subscript type 'list'" + (delete-file "tests/testthat/test_2d.R") + ;; "argument is of length zero" + (delete-file "tests/testthat/test_1d_gated_data.R")))))) (propagated-inputs (list r-biobase r-biocgenerics @@ -18940,7 +20734,7 @@ statistics to the plot.") (inputs (list gsl)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-flowworkspace r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description @@ -18953,14 +20747,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1vhp43l2iknljy240kzgvckkzbg186nkfdd1m3la9fnf9sqr33z9")))) + "1r9462sx6qfxbvrzzngcahg6mh77giapfvl16qswddn19jh8yc2g")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -18982,16 +20776,18 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.16.0") + (version "4.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0k22hifg4sv0xiw983gf1d6y7zkn9072famwj72x47w8vag4i0xz")))) + "0mjf3kzsmrrlg5asam96kjj8kqv12wn9xqbmf9pywgr5k6c045i7")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) + ;; Tests fail with: 'NA' is not a valid file + (arguments (list #:tests? #false)) (propagated-inputs (list r-bh r-biobase @@ -19014,7 +20810,7 @@ for other R packages to compile and link against.") r-scales r-xml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description @@ -19029,14 +20825,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.16.0") + (version "4.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "0q8g3sqmbhinfrb63yhv4lsczjz7pqwhwwsdlz2cg7s8yhp0cj6v")))) + "0lp8wmfgav47c7lqga9hykv5spwysv84dhvj4hvv13l0a10dd61a")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -19057,6 +20853,14 @@ matches the flowJo analysis.") r-ncdfflow r-rcolorbrewer r-rrcov)) + (native-inputs (list r-devtools + r-ggcyto + r-ggridges + r-gridextra + r-opencyto + r-scales + r-testthat + r-xtable)) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description @@ -19068,15 +20872,17 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "13ndjvm3l5pl1jgv7bqp78didqq3rx6br4p1ncqqp68mm048f2ll")))) - (properties `((upstream-name . "openCyto"))) + "07n5vv5jl34lc0l7ix952vararf6zwz3f64w1p32xnnkzvszpmiw")))) + (properties + `((upstream-name . "openCyto") + (updater-extra-native-inputs . ("r-flowworkspacedata")))) (build-system r-build-system) (propagated-inputs (list r-bh @@ -19093,7 +20899,7 @@ package.") r-rbgl r-rcolorbrewer)) (native-inputs - (list r-knitr)) + (list r-flowworkspacedata r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description @@ -19104,15 +20910,18 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "11kflx3yahl7xjl6x2rgpd4hl5y69qgarzhalmz4qdci7b7ln7kr")))) - (properties `((upstream-name . "CytoML"))) + "039rs6l92gjgvgh1nb8hfdg7h6dvak9hb5pjinli8x09iw08c463")))) + (properties + `((upstream-name . "CytoML") + (updater-extra-native-inputs . ("r-flowworkspacedata")) + (updater-ignored-native-inputs . ("r-old" "r-table")))) (build-system r-build-system) (inputs (list libxml2)) @@ -19137,7 +20946,12 @@ sequential way to mimic the manual gating strategy.") r-xml r-yaml)) (native-inputs - (list r-knitr)) + (list r-devtools + r-flowclust + r-flowstats + r-flowworkspacedata + r-knitr + r-testthat)) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description @@ -19148,14 +20962,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0xqrp184p00pvzzf6ddmp2r8lpg97bm0q6smjwcrfb8rn4msxmis")))) + "01dy2dxp1m6sx0wzy0q9axx2xrp30sqcjl4jhjnv8zxghk3m0frv")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -19174,6 +20988,7 @@ standard to exchange gated cytometry data with other software platforms.") r-rtsne r-tidyr r-xml)) + (native-inputs (list r-testthat)) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description @@ -19184,14 +20999,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.28.0") + (version "6.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "03pdg2hz4wnyigqakb9098ak9ww8fhwypzn006hfad0s042p9wvj")))) + "0bjwwjhcgbx27sm6ki3aag7jngmdsp3hr3hn58wkm492xa2hsimf")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -19202,6 +21017,7 @@ self-organizing map clustering and minimal spanning trees.") r-ggplot2 r-ggrepel r-gridextra + r-gsignal r-igraph r-lattice r-mass @@ -19209,9 +21025,10 @@ self-organizing map clustering and minimal spanning trees.") r-rarpack r-rcolorbrewer r-reshape2 + r-rgl r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description @@ -19230,14 +21047,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "15lpn1p2p28lhmzi7svszr0p1zkyaivi69q8pxcrv4lvips38hk4")))) + "0xxgkj672ncsp8dfa27cp101albvy4rq6f1jm0zmcmmf5lwc9v1m")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -19261,7 +21078,7 @@ delete entire rows with missing data.") r-robustbase r-viridis)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description @@ -19278,14 +21095,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1856jnvqacr12j5hnnl4w2abjjd7qvkz7cs8yhbnqpy1896wki0v")))) + "0iggn3p3i36xgl79dbs0nf9nv9cyiap7mlgg2s5q1fx9mni501xw")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -19303,7 +21120,7 @@ data, to only emphasize the data that actually matters.") r-tibble r-zoo)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description @@ -19321,19 +21138,19 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "05djywxsyfxb26d0clx51q7wmsw3rq56va444d6iy5n7xlhj9m94")))) + "1g86hffd0j3zyz654h0pn2pviykskkh40pcglf4bq99cxslnzww2")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description @@ -19355,7 +21172,7 @@ genes in the gene-set that are ranked above the leading edge).") (properties `((upstream-name . "CIARA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=CIARA") (synopsis "Cluster-independent algorithm for rare cell types identification") (description @@ -19367,14 +21184,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0x5ly5hkqli5b67hiaa6ha02damyps7vb4l51p0az1j5fxl39n8r")))) + "12j1j553pg5rd1ndg3xfjk9jgv2i72cck9pg74kylfhj5z2a1mfp")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -19400,7 +21217,7 @@ expression space.") r-tidyr r-vgam)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description @@ -19411,11 +21228,11 @@ accessibility data.") ;; This is the latest commit on the "monocle3" branch. (define-public r-cicero-monocle3 - (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") + (let ((commit "495ef0da13cc9ffe55516bfd34f48b671ad55aba") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") - (version (git-version "1.3.2" revision commit)) + (version (git-version "1.3.9" revision commit)) (source (origin (method git-fetch) @@ -19425,7 +21242,17 @@ accessibility data.") (file-name (git-file-name name version)) (sha256 (base32 - "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) + "0n1wgjirdfs9vwa37grmfdqmqb1nssa1r5xsssahg4049b126gn3")))) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'skip-bad-tests + (lambda _ + ;; FIXME 1 test fails with: "nrow(over) not equal to 98." + (substitute* "tests/testthat/test-runCicero.R" + ((".*find_overlapping_ccans works.*" m) + (string-append m "skip('guix')")))))))) (propagated-inputs (modify-inputs (package-propagated-inputs r-cicero) (delete "r-monocle") @@ -19434,14 +21261,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "0gjnx4645kd7qag7dzs5dp9lhsv6zg5xn6jna3bap4mginl1jvxi")))) + "0yszs0mzh9bdzaak1sqfypr05xn4nxy78g2b9m6rszxrf1g7k56b")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -19470,7 +21297,7 @@ accessibility data.") r-stringr r-universalmotif)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/Aufiero/circRNAprofiler") (synopsis @@ -19569,20 +21396,20 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0ijwyx42saqas52273c63c3yi948bh4pd4lifyqi3zjjs17bj1cg")))) + "0hc6vhlgd0p4f2cf2v2wbjfs068ag3ix1rrk91a25lj1mjnhh5ic")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-reshape2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description @@ -19593,14 +21420,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "074c6jg0dyr3hckizpg56f8ij8szj43cx6x5bbw7a01xdjdc70yb")))) + "1dmpi47pdxx0zfqvjc8najqr6qgqh6472qnsvycx44ldh5prl4lr")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs @@ -19615,14 +21442,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "19zlv9aglllsjq3jcnlw994bkanjdq0ib46k7wjsig04cx4apz1v")))) + "0806qbnkxzmyhx80x5ib7qkggqvcpvsm51n9s1cfplzsd7d5jb7i")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -19653,14 +21480,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0m5ws1qnbx7a3vj8bd9ggqi5w4icgzd5zi60qcy942j6zv4sswig")) + "0snq2n202gfzx4mk7h2nkmz48nralq3hr20qgarxmk6kcw97zav4")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -19690,7 +21517,7 @@ metrics, with methods for objects produced by the @code{methylumi} and (inputs (list lz4 xz zlib)) (native-inputs - (list r-knitr)) + (list r-biocgenerics r-digest r-knitr r-matrix r-runit)) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") @@ -19711,14 +21538,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0fa1dwbk6hdiwg6dmbks7hy4cg3ydyd2sv94cyl0003awhf00nn9")))) + "05l7kgjgjx4rk3vgffmmh5jrg8qx9bvr9bmq9f70w4bxx4kj6xry")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -19730,7 +21557,7 @@ with multiple R processes supported by the package @code{parallel}.") r-methylumi r-minfi r-watermelon)) - (native-inputs (list r-knitr)) + (native-inputs (list r-biocstyle r-knitr r-runit)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description @@ -19788,14 +21615,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "0yr4jfaxs253xg5q0kds8fm97kqacx67pw1c80yx2w79v7nqskgv")))) + "0sgnp5s5lgvkpypcbypls6lnav81d10r3kzyw61bva5xn236vwyx")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -19835,13 +21662,13 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-tilingarray (package (name "r-tilingarray") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tilingArray" version)) (sha256 (base32 - "1408275gvfilc2k8sfsja8bm5fdgnblf2sf5wdd3if51qi61clb0")))) + "13n4myj46zfb7y42phqqy7rmavr8793qg4l8wr04b0634b3dv4jf")))) (properties `((upstream-name . "tilingArray"))) (build-system r-build-system) (propagated-inputs @@ -19917,17 +21744,34 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "14kxlzgy71s8h34galx93q8kalspr1m23brssbr3wha0hxb0ghgd")))) + "0839ljb4fh1qrjk1xm89q2hwnbbxi2slaw3l36dk8kmpifhqqi16")))) (properties - `((upstream-name . "VariantFiltering"))) + `((upstream-name . "VariantFiltering") + (updater-extra-native-inputs + . ("r-biocstyle" + "r-bsgenome-hsapiens-1000genomes-hs37d5" + "r-org-hs-eg-db" + "r-txdb-hsapiens-ucsc-hg19-knowngene")))) (build-system r-build-system) + (arguments + (list + ;; Vignettes require an obscene amount of humongous annotation packages + ;; and *still* attempt to download additional files off the Internet. + ;; Enough is enough. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test tries to connect to a website. + (delete-file "inst/unitTests/test_location-methods.R")))))) (propagated-inputs (list r-annotationdbi r-biobase @@ -19953,6 +21797,12 @@ provides methods for retrieving enriched pathways.") r-summarizedexperiment r-variantannotation r-xvector)) + (native-inputs + (list r-biocstyle + r-bsgenome-hsapiens-1000genomes-hs37d5 + r-org-hs-eg-db + r-runit + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://github.com/rcastelo/VariantFiltering") (synopsis "Filtering of coding and non-coding genetic variants") (description @@ -19964,14 +21814,14 @@ populations, splice site strength, conservation, etc.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.34.0") + (version "1.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "00hrizpx05jfh7yrab6na10zkahm8ibrbxy4pa4dcldw65klqmn9")))) + "1k6xcvwam6rzzj9inrz9qwqarh734ray2hfjzljah653nznnmbdi")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -19998,7 +21848,7 @@ populations, splice site strength, conservation, etc.") r-rlang r-scales)) (native-inputs - (list r-knitr)) + (list r-edger r-knitr r-rfast r-runit)) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description @@ -20043,13 +21893,13 @@ features (e.g. genes, microRNAs).") (define-public r-ucell (package (name "r-ucell") - (version "2.8.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "UCell" version)) (sha256 (base32 - "09r64rrydwgvvvq8f5vzvn7dsh24l9sa1if21wcimrl28ci1g1mv")))) + "11fxdfyxnq6kvsp9iklb4wqywlplgi9s4nnz6qpr8ssbqqjlsm0c")))) (properties `((upstream-name . "UCell"))) (build-system r-build-system) (propagated-inputs (list r-biocneighbors @@ -20074,17 +21924,17 @@ directly interact with SingleCellExperiment and Seurat objects.") (define-public r-ucsc-utils (package (name "r-ucsc-utils") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "UCSC.utils" version)) (sha256 - (base32 "0w9f5xd6ryniapbpcrpczn8wimph2154w45cvdgqfa3dv5qy379l")))) + (base32 "14nyaqwz1mvaab5kj63j8h56f2n14v6dz5l1nl9zpp4icgx9hp64")))) (properties `((upstream-name . "UCSC.utils"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/UCSC.utils") (synopsis "Low-level utilities to retrieve data from the UCSC Genome Browser") @@ -20100,19 +21950,19 @@ txdbmaker.") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.38.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "0v3jpnm3nq66xvckmc8447xl7wngfhhiwq6vjx54wgc6f586vmgd")))) + "174dj0vkccabi89jf3ld39ksl6gds9q5kadyrqvvmnp5ic9h59wj")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) (propagated-inputs - (list r-biocgenerics r-htqpcr)) + (list r-biocgenerics r-limma)) (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") (description @@ -20124,14 +21974,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.22.2") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "12svaygg47j5smay57j5lkxj8llky1fm4s8ni0nzikq5a9j47w5y")))) + "03wjwi3h6agdvp552cd8mlrlvjjb1wwi0z02yclh0jcxbrd7a90z")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -20155,7 +22005,7 @@ data.") r-s4vectors r-yaml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/universalmotif/") (synopsis @@ -20173,13 +22023,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "1gpn9z09cfcy2mj7m32xfb2bjjwl01g9qn9nqaivmqbi4k6icrr8")))) + "0ky6l0x5wbwil0lqnclgfpdhn94954k62xpv0z3mhy4lvqf07h4j")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) @@ -20202,13 +22052,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "00dcx6kcqq5xcdy7rqgi51cvc20dsgrrki8aicbj1icx0m6601wa")))) + "1z9phvx461s64i251rvxwr9x62mm18pc0qlifzr8z4ybmlrbyazi")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) @@ -20226,13 +22076,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0jak83dlavhczaa2nqk5g2l0h4grnc9v24bg6v9mjfn6bqhl1s7j")))) + "05lvljiq3wgn0xqax8nhrsfwfxkslch9fyzk8v7qdvi72j0j3g9b")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) @@ -20253,16 +22103,19 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "1h3drjxdmd837hc7l1xk6b4ha39i7bqkb8862h4h6s5rfa7dcc50")))) + "0x49x7xyjwfw5zf4w4rchapnb40mr1c6shj5cdsg9cbwwdz971ws")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) + ;; FIXME One test fails. + (arguments (list #:tests? #false)) (propagated-inputs (list r-boot)) + (native-inputs (list r-biocgenerics r-runit)) (home-page "https://bioconductor.org/packages/acde") (synopsis "Identification of differentially expressed genes with artificial components") @@ -20303,7 +22156,7 @@ rate} (FDR).") r-iranges r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description @@ -20332,7 +22185,7 @@ using whole genome sequencing data.") (propagated-inputs (list r-data-table r-ggplot2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") (synopsis "Multivariate pathway enrichment analysis") (description @@ -20441,14 +22294,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0397xg4sj988b0chzfpy23dszpjbdkch59wfynbn4pwyvl0qmp9j")))) + "1x8fxcv8lvclb3ynj16gld6l07jdqlarrk1j26g5bsqy0zd0v7gm")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -20463,20 +22316,20 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "148j41mawxvzyal9lfjy7h1gp0w8zwmgc7s32wiqa30qjcc82snx")))) + "0p5ziib0k8clv8jk99k1z6izk63fpklb6nkf40ar4i63ri4yp776")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs (list r-genomicranges r-poibin)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description @@ -20492,14 +22345,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "02pmxg0ppy1asjscp13kmqyj2phw4q138fj2b3xgmcagwxqzb4bs")))) + "0ygjcg7z0shajswp5bfavslq2b4hdxy30d7bb5i5a11kzxymwg3h")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -20518,13 +22371,13 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hybridmtest (package (name "r-hybridmtest") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HybridMTest" version)) (sha256 - (base32 "0fh0v29fpwzramqnbxmzpmgiziwswdx38734g2lx303b0blkbv7j")))) + (base32 "14i9pvs4fpiw6bv6lrj8v4sc4y848a566cn2ia3lpsfs0naf79gk")))) (properties `((upstream-name . "HybridMTest"))) (build-system r-build-system) (propagated-inputs @@ -20549,18 +22402,19 @@ then the law of total EBPs.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "12g33rw1qy1ij32k87qrw04pak20p8z04mch9lxjy5yrj5k5x812")))) + "1928iia8l2sanirzb22i67n71zsnbps0qbdsf6ll7zpvs2vcmd5c")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs (list r-graph)) + (native-inputs (list r-runit)) (home-page "https://bioconductor.org/packages/hypergraph") (synopsis "Hypergraph data structures") (description @@ -20571,14 +22425,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "104xwij9vq5gwq4ml7fnhsp4apcldbgxmhppwklg6zqdfixpmig5")))) + "0p98gicscijllmhb302jca1z04xvm9rcrsnz429c3d8rckz3asr9")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) @@ -20593,14 +22447,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1ja5j9753rgx61jwkax0mzkxh7ybh3m4ampkr5ikw3afda23wg1z")))) + "0zvazxkyllalb2j3k6hwh1g1p0jbm2kcn0yf9ypi8v5wfw71c5dc")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -20637,7 +22491,7 @@ networks and estimated fluxes can be visualized with hypergraphs.") (propagated-inputs (list r-bigmemory)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description @@ -20667,6 +22521,8 @@ a file-backed matrix with factor properties.") "1r9gr5f9as09ifagal5k7713h95qjw508cf8ny3j1jmqd24v6xhs")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) + ;; 4 tests fail with "cannot xtfrm data frames" + (arguments (list #:tests? #false)) (propagated-inputs (list r-delayedarray r-dplyr @@ -20687,7 +22543,7 @@ a file-backed matrix with factor properties.") r-summarizedexperiment r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://github.com/lindsayrutter/bigPint") (synopsis "Big multivariate data plotted interactively") (description @@ -20700,17 +22556,21 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemmineob (package (name "r-chemmineob") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineOB" version)) (sha256 - (base32 "17yvmdg16pb1dmx160n6vcgw3sa1yf40f8yzivdyic3sckn4z4bw")))) + (base32 "0nvlc2s5s9w7zqalay6dz73mqrcalbkyv43jx52pcgnl842r4g95")))) (properties `((upstream-name . "ChemmineOB"))) (build-system r-build-system) (arguments (list + ;; Tests require r-chemminer; adding it would lead to mutually recursive + ;; dependency declarations. The tests also complain that Cairo is not + ;; loaded. + #:test-types '(list "vignettes") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'patch-makefile @@ -20724,7 +22584,7 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") "/include/eigen3")))))))) (inputs (list eigen openbabel)) (propagated-inputs (list r-bh r-biocgenerics r-rcpp r-zlibbioc)) - (native-inputs (list pkg-config r-knitr)) + (native-inputs (list pkg-config r-knitr r-runit)) (home-page "https://github.com/girke-lab/ChemmineOB") (synopsis "R interface to a subset of OpenBabel functionalities") (description @@ -20741,14 +22601,14 @@ add-on package rather than used directly.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.56.0") + (version "3.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1252xy33bgjrd4gh4shrgzklgxry2lf67svzxjra5yckf8am0rdc")))) + "0gydxqchyhgx1jq4p3658dvhiqpmwhynngcmpkac9sim9ym968db")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -20768,7 +22628,7 @@ add-on package rather than used directly.") r-rsvg r-stringi)) (native-inputs - (list r-knitr)) + (list r-knitr r-chemmineob r-rsqlite r-runit r-snow)) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description @@ -20784,18 +22644,18 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "080src34jwkvbk98pa4ri530l9gi4ibr5mwxib1681np0cfal54g")))) + (base32 "1zd5frijcxyv9k3v5irzrzx7wvhlwx6c395r2pai37pxzdxr1m4a")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-chemminer r-runit)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://github.com/girke-lab/fmcsR") (synopsis "Mismatch tolerant maximum common substructure searching") (description @@ -20813,14 +22673,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0rckhgg73cgz0ppqaywc7nvbnp1is6cyjfa7dn2l32xxrcl57pq6")))) + "0zxrmxsq3hvim288w16029xazk3fksiwdl444f211yyfhwkb1n31")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -20832,7 +22692,7 @@ searching and clustering.") r-rsqlite r-xml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/girke-lab/bioassayR") (synopsis "Cross-target analysis of small molecule bioactivity") (description @@ -20848,20 +22708,20 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "0flj14d8aamr1fzcpd0k7jq5rs0j5dsijpahg066qrnapn5990d0")))) + "1ihzrx46320fxhbxvxk4c87bidvj2m2cy6qxya61n7p807qqq76q")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-broom r-dplyr r-tidyr)) (native-inputs - (list r-knitr)) + (list r-deseq2 r-edger r-knitr r-testthat)) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description @@ -20877,19 +22737,21 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "1xymgghgj4r1k9i73zqgava79l0djz945jnl5ad193flv13fpdgs")))) + "0ayqhz94qri62m0rs1x7q59s7wl4winqlahrwwd0k8qylgz9yx6b")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) + ;; Tests need internet access. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-graph r-httr r-purrr r-rappdirs r-rlang)) - (native-inputs (list r-r-rsp)) + (native-inputs (list r-checkmate r-r-rsp r-testthat)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -20901,14 +22763,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "0i5jrdzg6zcs1jx0lryq8d467lxi1hvd1x6p74ywwxga88p46zk6")))) + "15l2j7jhwr3f024h3px18z9kgva3g0kghgwm8gy9dp5ljdz68d4w")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -20920,9 +22782,10 @@ symbols).") r-graphite r-gson r-igraph - r-reactome-db)) + r-reactome-db + r-yulab-utils)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description @@ -20934,14 +22797,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "17ym1y90bz85afanggdjf91a49lz89qmmi2kyhxga0cw056lkdz0")))) + "1wzfi2bfzhdjc5nvs1iwb8b7ln0n9fhkvpqf27y3p082ajhybjdf")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -20956,13 +22819,13 @@ microarray data.") (define-public r-biocbaseutils (package (name "r-biocbaseutils") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocBaseUtils" version)) (sha256 (base32 - "0f8bzhpi6xla52sbvpd20sgli7mp5xfk2aqpcv6jkf8s59jsmn54")))) + "10xzfxyl12zkcx8l0b5hnmcnq6bdr1gg1dp64indvrnwwqpdjqjp")))) (properties `((upstream-name . "BiocBaseUtils"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -21000,13 +22863,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0rvr68d5anir7bj913nxwwfj7i3h2dvadcfvjjdbdr3m35wyx1g8")))) + "0c0gwa2wxwfh8ypj1vgy5lp89msn2s9cd155mwn0ginabvp9v36r")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -21016,6 +22879,7 @@ monograph.") r-biocmanager r-biocviews r-callr + r-cli r-codetools r-graph r-httr2 @@ -21033,14 +22897,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "0ji6pa8wfj57drpnp03vgas1pird84g15nnp6469jmx773izhfq0")))) + "13k619dazrrfh52pmq6jqx3q2sr3jx5jilbvkbn4yk55md6dxjcy")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -21055,20 +22919,49 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1m0nn2m548726w576mx8mx29xj428q1rkpn7z7a7m8kzgcvvgkkr")))) + "1n6dg53sx1vmz2xzfj040l26znp3664wcam92nxm7hsi0l5lbqyx")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) (propagated-inputs (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml)) (native-inputs - (list r-knitr)) + (list ghostscript + r-biocgenerics r-knitr r-runit + (texlive-updmap.cfg + (list texlive-bera + texlive-booktabs + texlive-caption + texlive-changepage + texlive-enumitem + texlive-etoolbox + texlive-etoolbox + texlive-fancyhdr + texlive-fancyvrb + texlive-footmisc + texlive-framed + texlive-geometry + texlive-helvetic + texlive-marginfix + texlive-mathtools + texlive-nowidow + texlive-parnotes + texlive-parskip + texlive-pdfcrop + texlive-placeins + texlive-preprint ;authblk + texlive-ragged2e + texlive-soul + texlive-titlesec + texlive-titling + texlive-xcolor + texlive-xstring)))) (home-page "https://bioconductor.org/packages/BiocStyle") (synopsis "Bioconductor formatting styles") (description "This package provides standard formatting styles for @@ -21079,16 +22972,18 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "10j9s50ppfx8r752wkabls0n4gxp17z7dnaf352f3dcdbfa8ijh5")))) + "0y1i7sl76kczmkynb2lyd7v6mmz4gfp3j1qp4w4swn221q5p1cjr")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) + ;; Tests attempt to access http://bioconductor.org/js/versions.js + (arguments (list #:tests? #false)) (propagated-inputs (list r-biobase r-biocmanager @@ -21097,7 +22992,7 @@ functionality.") r-rcurl r-runit r-xml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -21108,14 +23003,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "0mj1aqxyp84mn5m0fwk9lijysy594hhga3kv4mddv45vqxdsr08h")))) + "1zawq85nffj4jvq2yvrgrxph4vhi2fjw2sc4qll0r45pdkx4vjr4")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -21141,13 +23036,13 @@ access.") (define-public r-experimenthubdata (package (name "r-experimenthubdata") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHubData" version)) (sha256 - (base32 "1adm3b0nacbdi4x5z71iiif9d876m3ip6crhbbr2hw4mbk6is7qn")))) + (base32 "1bg11hpmia4gbzslvlawrq8z5ycyx0sby9sg678x881zkaf107fm")))) (properties `((upstream-name . "ExperimentHubData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhubdata @@ -21158,7 +23053,7 @@ access.") r-experimenthub r-httr r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/ExperimentHubData") (synopsis "Add resources to ExperimentHub") (description @@ -21196,17 +23091,24 @@ db and resource files to AWS S3 buckets.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0spws2kawf5rqhp5h5wi46sa07c2yhhnjhdxpmxz8gkvqsvdjqkp")))) + "1lsnw4w0ln4596vwd4a69nnhmnf7z05brpisripjisjrgr374sgy")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; For vignette builder. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-biobase r-biocbaseutils @@ -21218,7 +23120,12 @@ db and resource files to AWS S3 buckets.") r-summarizedexperiment r-tidyr)) (native-inputs - (list r-knitr r-r-rsp)) + (list r-hdf5array + r-knitr + r-r-rsp + r-raggedexperiment + r-reshape2 + r-testthat)) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description @@ -21230,69 +23137,23 @@ classes for individual assays, and allowing subsetting by genomic ranges or rownames.") (license license:artistic2.0))) -(define-public r-bioconcotk - (package - (name "r-bioconcotk") - (version "1.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "BiocOncoTK" version)) - (sha256 - (base32 - "0h4cr7lrmbyx7kdj81s7ff75svr01rvzn54svqi93vjilawmpbm3")))) - (properties `((upstream-name . "BiocOncoTK"))) - (build-system r-build-system) - (propagated-inputs - (list r-bigrquery - r-car - r-complexheatmap - r-curatedtcgadata - r-dbi - r-dplyr - r-dt - r-genomicfeatures - r-genomicranges - r-ggplot2 - r-ggpubr - r-graph - r-httr - r-iranges - r-magrittr - r-mass - r-plyr - r-rgraphviz - r-rjson - r-s4vectors - r-scales - r-shiny - r-summarizedexperiment)) - (native-inputs - (list r-knitr)) - (home-page "https://bioconductor.org/packages/BiocOncoTK") - (synopsis "Bioconductor components for general cancer genomics") - (description - "The purpose of this package is to provide a central interface to various -tools for genome-scale analysis of cancer studies.") - (license license:artistic2.0))) - (define-public r-biocor (package (name "r-biocor") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "0jpi51f9cv3sv4l69974bba8c8k0inb6zxviv7i907ldaiiblr07")))) + "0f282cfs326xj0dib57wqclqj0gnllqxm8zcy0s23qx5kb4jzq08")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-gseabase r-matrix)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description @@ -21306,14 +23167,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1nbzr1yjz65r0y8c312hnvagnc1pdgda4v6sxbpvlkl3z93jsy6x")) + "0d0acbhqm7x7813jmm90hw9fmv559zrahxnlm6smaw3jz74kb2q4")) (snippet '(for-each delete-file '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js" @@ -21324,6 +23185,8 @@ gene selection, testing relationships, and so on.") (build-system r-build-system) (arguments (list + ;; Tests attempt to connect to the internet. + #:tests? #false #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) @@ -21375,6 +23238,7 @@ gene selection, testing relationships, and so on.") (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) ("js-bootstrap" ,(origin (method url-fetch) @@ -21383,6 +23247,7 @@ gene selection, testing relationships, and so on.") (sha256 (base32 "07fm28xbkb7a5n7zgmfxgbl2g5j010r4gvc54y79v1f119s3kz6y")))) + ;; 3.5.17 ("js-d3" ,(origin (method url-fetch) @@ -21420,16 +23285,26 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1r1if1k7qgni3dk7gsl4vcyvd6hnhx94rcq5yi9w7dvyyrbvnwwa")))) + "1jl4q3r6zcn837kd627wfki6z42bxdfklrj97c4r3cr3bnbyxvk0")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test tries to connect to a website. + (delete-file "tests/testthat/test_mapping_set.R") + ;; One test fails with a sorting error. + (delete-file "tests/testthat/test_BiocSet-methods.R")))))) (propagated-inputs (list r-annotationdbi r-biocio @@ -21442,7 +23317,7 @@ analytics on packages.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-gseabase r-knitr r-org-hs-eg-db r-testthat)) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis @@ -21458,14 +23333,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1gw0lmdhkzp5ar54yv9jagqmpxp7j9ajfmdqb2y2qrnhh39hymzs")))) + "195n6va4y1caj9g5dzdimzdi7ygkapmiq0cxd1lzk8sf2skg5dwb")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -21491,14 +23366,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "1yxr5df1y8v5c9imh27j86s7g9wjvi51j2wyn8jgma875mad41hq")))) + "0c2dwb6znpfcfcz5nxjvi4scs4nhn4h42gb48jhnyz4p2i96rmqb")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -21513,14 +23388,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "04a1fvwgqxzf7992lyh9qzz2z2fgmfwfjvpw5xr21pcrpas57l2r")))) + "12w8jqadfcnvavhiksxs8sc8lg4k6053gl5czamdssqb2rqiy14l")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -21538,7 +23413,7 @@ distance measures.") r-matrix r-rcpp r-reshape2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-scran r-testthat)) (home-page "https://github.com/kevinblighe/PCAtools") (synopsis "PCAtools: everything Principal Components Analysis") (description @@ -21559,14 +23434,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0sszyfnnzzn5xhs39zgkzr7f3da820nxr6qaw68wknblgmyyddi8")))) + "0rrnsfbbxxz6j1glp7bmffc4gwf0wwk5bw5lfy3rv8mwq2szgks9")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs @@ -21593,7 +23468,7 @@ dimensional mass cytometry data.") r-shiny r-txdb-hsapiens-ucsc-hg19-knowngene r-txdb-hsapiens-ucsc-hg38-knowngene)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") (description @@ -21605,14 +23480,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "1h3zxb3m68lq37g25zqxpmk2c9yrdhydyhh7ad2d30hif73qiacm")))) + "11ll6ry20qmiciw2ma5rqbmggd9ahxddk24sh7mqxkrw1c1im760")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -21638,14 +23513,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "16bblkxp8pj7qaxfzmp30lfj8vy13d3q8cf5y0g40lk4rbldx3bz")))) + "0f07k20dg3hdwg4q67yg2n9q8carddz135g6p15admz2bmdx7lsy")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -21761,17 +23636,19 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1cd91iakbpf2hjysc44sqqrah63cgq4fz3n8j81virfwl3ir95xm")))) + "0qpvyg5wjgf1bf1h2mripbsn03by3nap0561kk8qsxg4q71bdnah")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) + ;; Tests fail with: "return code from pthread_create() is 22" + (arguments (list #:tests? #false)) (home-page "https://github.com/bmbolstad/preprocessCore") (synopsis "Collection of pre-processing functions") (description @@ -21782,13 +23659,13 @@ routines.") (define-public r-s4arrays (package (name "r-s4arrays") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Arrays" version)) (sha256 (base32 - "0wdzp1q6hyks4afm217yl2n770jsqaqxix71imni1r0qbxdfkdwl")))) + "0fjf1q9wlm8n1w8sb9n0yx6s1di33ngk4kanhychy5hqli73v3dh")))) (properties `((upstream-name . "S4Arrays"))) (build-system r-build-system) (propagated-inputs @@ -21798,7 +23675,7 @@ routines.") r-iranges r-matrix r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/S4Arrays") (synopsis "Foundation of array-like containers in Bioconductor") (description @@ -21819,16 +23696,18 @@ array-like semantic. It also provides: (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.42.1") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "080fr8f4lqzvn73y50wgz19w0a0hvkd9ilwswmv5gi34sihp8795")))) + "0wic4nri42yiasshal96ykxj8skrya5szffnawqzs1kmq2b8zail")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) + ;; Tests require r-iranges, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocgenerics)) (native-inputs (list r-knitr)) @@ -21849,14 +23728,14 @@ S4Vectors package itself.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.72-5") + (version "1.73") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "17g7lan1rpy6y4nmqksrf9ddp3gs58vdczfavgq1fp13zx1r2hq3")))) + "1kk3a2ll83zdwisjfvg4km5h0vl564nshy45ffgxv41im5ks7878")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -21887,14 +23766,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "09i174a867vqyb6677sj88lk6bpfc4ajsmjgjkd7f7q66j46q655")))) + "0jljp88rxdq16b1976g77ix5x61ajr60fjf20wp9j17x4q9h2c1p")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -21905,8 +23784,7 @@ data manipulation and visualization.") ;; The replacement value is taken from src/graphviz/builddate.h (substitute* "src/graphviz/configure" (("VERSION_DATE=.*") - "VERSION_DATE=20200427.2341\n")) - #t))))) + "VERSION_DATE=20200427.2341\n"))))))) ;; FIXME: Rgraphviz bundles the sources of an older variant of ;; graphviz. It does not build with the latest version of graphviz, so ;; we do not add graphviz to the inputs. @@ -21914,7 +23792,7 @@ data manipulation and visualization.") (propagated-inputs (list r-graph)) (native-inputs - (list pkg-config)) + (list pkg-config r-runit r-xml)) (home-page "https://bioconductor.org/packages/Rgraphviz") (synopsis "Plotting capabilities for R graph objects") (description @@ -21925,13 +23803,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "02lzx8whxd3z4k0saf0vaq4np8lag00nkp3hd6da1w91vczs1kjl")))) + "07qzplkpq1zbh671b44c1qa1k47jqqmyrrrdyixjz0fqj0ikw6ya")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (propagated-inputs @@ -21947,7 +23825,7 @@ objects from the @code{graph} package.") r-singlecellexperiment r-summarizedexperiment r-svmisc)) - (native-inputs (list r-knitr)) + (native-inputs (list r-data-table r-deseq2 r-knitr r-samr r-testthat)) (home-page "https://github.com/mikelove/fishpond") (synopsis "Downstream methods and tools for expression data") (description @@ -21961,13 +23839,13 @@ working with Salmon and Alevin quantification files.") (define-public r-fithic (package (name "r-fithic") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "107hm9k9wfr34fradldmjym2bzxb6qx8109p4a7xrqkiya0hmwwa")))) + "166djgps0k8xb9rjx8i6sfh71a4cqkgpkw3dr25plprafj4qlxva")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -21985,13 +23863,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0nxk3rdfw78bwyxjd3bbm093i8hqyk63rz0fvx3fi04qpa1fv39r")))) + "0y5qlr36pj7mrgs70v4zf9s19rpa11mzyagmpxs77n0pl9nrhgwj")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -22014,18 +23892,25 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1cfm15zwfp1gxgrkknyvdaqb5fm27s2nyjrhxwkrbn32yfdrgdnz")))) + "1jkrlmnsf5ncs4l77b29p8cjn6nmaadpvrsn5z1qixsw1axbqwi0")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) - (inputs - (list)) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This file depends on r-zellkonverter, which uses r-basilisk to + ;; set up a Conda environment. We don't want that. + (delete-file "inst/unitTests/test_H5ADMatrixSeed-class.R")))))) (propagated-inputs (list r-biocgenerics r-delayedarray @@ -22035,7 +23920,12 @@ provided.") r-rhdf5filters r-rhdf5lib r-s4arrays - r-s4vectors)) + r-s4vectors + r-sparsearray)) + (native-inputs + (list r-biocparallel + r-runit + r-singlecellexperiment)) (home-page "https://bioconductor.org/packages/HDF5Array") (synopsis "HDF5 back end for DelayedArray objects") (description "This package provides an array-like container for convenient @@ -22046,14 +23936,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0q4ix3nzr69pmwm6vdna51yxlqi8frch0xyv6wmiy35n67d4fcab")) + "0l9hq7444azc72h3185qch053a9rvm89aagisrsn01k5c32jwk9r")) (modules '((guix build utils))) (snippet '(begin @@ -22127,19 +24017,33 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0gvxz9w2mi8scqyyhhnrasscs7hwvxxlqvh7j9m6akpi8qq91v6y")))) + "0w1abs9nwpn66zc81alnzvdrg5y5w0sl2qdqw6bx3hp0ry1sjfr5")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-bad-test + (lambda _ + ;; This test would require r-beachmat-hdf5, but that package + ;; depends on r-beachmat. + (delete-file "tests/testthat/test-initializeCpp-other.R")))))) (propagated-inputs - (list r-biocgenerics r-delayedarray r-matrix r-rcpp r-sparsearray)) + (list r-assorthead + r-biocgenerics + r-delayedarray + r-matrix + r-rcpp + r-sparsearray)) (native-inputs - (list r-knitr)) + (list r-biocparallel r-hdf5array r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -22147,16 +24051,45 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +(define-public r-beachmat-hdf5 + (package + (name "r-beachmat-hdf5") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beachmat.hdf5" version)) + (sha256 + (base32 "0jla4by5y8qalswfam348p2459lk191x4p057w24jqgcf98gbbhg")))) + (properties `((upstream-name . "beachmat.hdf5"))) + (build-system r-build-system) + (propagated-inputs (list r-assorthead + r-beachmat + r-delayedarray + r-hdf5array + r-rcpp + r-rhdf5lib)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://bioconductor.org/packages/beachmat.hdf5") + (synopsis "beachmat bindings for HDF5-backed matrices") + (description + "This package extends beachmat to support initialization of tatami +matrices from HDF5-backed arrays. This allows C++ code in downstream packages +to directly call the HDF5 C/C++ library to access array data, without the need +for block processing via @code{DelayedArray}. Some utilities are also +provided for direct creation of an in-memory tatami matrix from a HDF5 file.") + (license license:gpl3))) + (define-public r-beadarray (package (name "r-beadarray") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beadarray" version)) (sha256 (base32 - "0yda6maj985k374bh6zkrs8qffw1jrz9gc3mja07ibyn4pvzkclq")))) + "1khlljv6q32y2jg17g3lf6hvjs36ld27nasv03vlq7mb61pgda7d")))) (properties `((upstream-name . "beadarray"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -22203,13 +24136,13 @@ performs copy number calculations and reports.") (define-public r-beaddatapackr (package (name "r-beaddatapackr") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BeadDataPackR" version)) (sha256 (base32 - "0wz3prri0mfjczmb432faxfjc99wg4lq26l3a60rmxyxq8mcnpkv")))) + "0qzgn3kj7137yp8crj4d8ir597c5k0qscg7n7fdzhi7540jjnpsb")))) (properties `((upstream-name . "BeadDataPackR"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -22226,13 +24159,13 @@ decompression of raw bead-level data from the Illumina BeadArray platform.") (define-public r-cner (package (name "r-cner") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "19kfh7p8zlb1nbwpsj6i1b7pqy829dij7n7iavznhxw44cmif6sv")))) + (base32 "0f4hbg5vprsygpd3d79vrvz2d35rbicv5wgllnk5cyvyrgsp15c7")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) @@ -22258,7 +24191,7 @@ decompression of raw bead-level data from the Illumina BeadArray platform.") r-s4vectors r-xvector)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ge11232002/CNEr") (synopsis "CNE Detection and Visualization") (description @@ -22275,14 +24208,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0bmmsgmx7159bdrflykkis0v4z1ixwlnmw1kx0y0kw15lw3cjnsh")))) + "129qkllv3i0pifigw255g3k4b6ki6sf8hql56x2nbm6h64bcfd9c")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -22307,7 +24240,7 @@ advanced visualization of sets of conserved noncoding elements.") r-tfmpvalue r-xml r-xvector)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ge11232002/TFBSTools") (synopsis "Transcription factor binding site (TFBS) analysis") (description @@ -22322,18 +24255,19 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "0c2sf8l1wfgz3nh9ccm10y9wwh7rv55r09awavqlrr9glcbblp32")))) + (base32 "0vdqasrb4j7cvp66df2fvjbdi65480zrdzbbv057nlkvq1h4m3p3")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-dnacopy + r-pheatmap r-rcolorbrewer r-rhtslib r-survival @@ -22351,14 +24285,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1wpvdg5x51cbzpqa4s2s0zl9h7fsrsp87mxxlhxs65zx6yyfj2xl")))) + "0a2hd7fld7q22kpllpq6zb79ivpfrrq1vz1v4fariar18800fjc2")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -22374,7 +24308,7 @@ customizable visualzations with minimal effort.") r-s4vectors r-summarizedexperiment r-tfbstools)) - (native-inputs (list r-knitr)) + (native-inputs (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/motifmatchr") (synopsis "Fast motif matching in R") (description @@ -22385,13 +24319,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "092y1x1sbqvjrwmr7sv2r5216wbwwc4lk6kwn57fnvvdnc0hc3sv")))) + (base32 "0mv8bfjr80k3nmmy0vsvjsrb4hi7n4adazmzgf6xi3hiiyajiv87")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -22417,7 +24351,7 @@ This package wraps C++ code from the MOODS motif calling library.") r-shiny r-summarizedexperiment r-tfbstools)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") (synopsis "Determine chromatin variation across regions") (description @@ -22432,14 +24366,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "09sbk0r9g55x8fbvv5rbrygdw3km4bbrj9x0abqwld2nxnxq1q3n")))) + "1kaxlhfg2c2vdvd1bw24qrxh2ffzxrxmd51znrisrhpvjl7r53jx")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -22447,7 +24381,7 @@ sequence (@code{DNAse-seq}) experiments.") (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -22460,17 +24394,18 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0l33bsi1zfj7f4hzlivhh89phhx0qscrwd08c28mqvcyp91mhq16")))) + (base32 "1dlawx0hxnbb955yhbq4ryxv5yi62hgzh5di9vrzx1pi14vnc5nk")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs - (list r-beachmat + (list r-assorthead + r-beachmat r-biocneighbors r-biocparallel r-biocsingular @@ -22480,7 +24415,8 @@ libraries.") r-rcpp r-s4vectors r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-knitr r-scuttle r-singlecellexperiment r-testthat)) (home-page "https://github.com/LTLA/SingleR") (synopsis "Reference-based single-cell RNA-seq annotation") (description @@ -22492,14 +24428,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1cja56k5y5vi1x0jdxaxvh13fc2lzh8g30gp294pz6p61prrf3ws")))) + "0h13a9pgsm3w324622qlp9nqpvq6gsjwcyd44d6w5yzrl9jcsliv")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -22507,14 +24443,16 @@ cell types to infer the cell of origin of each single cell independently.") r-biocgenerics r-biocparallel r-delayedarray - r-delayedmatrixstats r-genomicranges r-matrix + r-matrixgenerics r-rcpp + r-s4arrays r-s4vectors r-singlecellexperiment + r-sparsearray r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/scuttle") (synopsis "Single-cell RNA-Seq analysis utilities") (description @@ -22527,13 +24465,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1052jlflk596q8dbzhwx150ql53lhz109lljc011ni42a5zvjnbm")))) + "1b4sc5gi2wjcrfm78y0w7df2bb5sw6spjswhsss47shxy6m2vhh1")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -22556,11 +24494,12 @@ of other packages.") r-s4vectors r-scuttle r-singlecellexperiment + r-sparsearray r-summarizedexperiment r-uwot r-viridis)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -22571,14 +24510,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0s1y2q4v596wxh8p5sr43mk9cnsc4kg36ld7vx71hbn3hwscqaa1")))) + "1gi5sv5bb7y8r95sr7cc01cy01j1ymc9piyjmriz0ybyh8flwyrv")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -22588,21 +24527,22 @@ quality control.") r-biocsingular r-bluster r-delayedarray - r-delayedmatrixstats r-dqrng r-edger r-igraph r-limma r-matrix + r-matrixgenerics r-metapod r-rcpp + r-s4arrays r-s4vectors r-scuttle r-singlecellexperiment r-statmod r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-delayedmatrixstats r-hdf5array r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -22614,13 +24554,13 @@ variable and significantly correlated genes.") (define-public r-sparsearray (package (name "r-sparsearray") - (version "1.4.8") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SparseArray" version)) (sha256 - (base32 "1ahwv6ih1700h1sccv9wh7hr5bhdif0ji5jbmsprnhjxfgn6xidm")))) + (base32 "0bd5f9p94w73c9vwbvlnkvpl11d8jg2c7l6b0pcx4zdxrqv4yi07")))) (properties `((upstream-name . "SparseArray"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -22631,7 +24571,7 @@ variable and significantly correlated genes.") r-s4arrays r-s4vectors r-xvector)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/SparseArray") (synopsis "Efficient in-memory representation of multidimensional sparse arrays") @@ -22651,20 +24591,20 @@ in the @code{matrixStats} package from CRAN.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "04hk9r6sh83dyxm2j7jdcj0m4g74ln218j21rs71c2gg6mrkmlgf")))) + "0gmp2pwypl1bx0584xy2rv65fkk907g12k71jc76n94mk6lr1q75")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-matrixgenerics r-matrixstats r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/sparseMatrixStats/") (synopsis "Summary statistics for rows and columns of sparse matrices") (description @@ -22676,15 +24616,21 @@ data in the column sparse format.") (define-public r-spatialexperiment (package (name "r-spatialexperiment") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SpatialExperiment" version)) (sha256 (base32 - "0f04azs6wscibcpbmc1m21wjswmgr2b8gvd1n2yavya1li0xxm4r")))) + "02lsz2yag9h94ylwsdbqwvlsdgx6ijz9702hg5prz122jqv7x9l3")))) (properties `((upstream-name . "SpatialExperiment"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-biocfilecache r-biocgenerics r-magick @@ -22692,7 +24638,7 @@ data in the column sparse format.") r-s4vectors r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-dropletutils r-knitr r-testthat)) (home-page "https://github.com/drighelli/SpatialExperiment") (synopsis "S4 class for spatially resolved -omics data") (description @@ -22707,14 +24653,14 @@ Visium platform.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1cqf6y0f18469v1jgfvdjnskkc89i3sfg79axxqcwa33mfjj736s")))) + "01yrbmdj38r6h4n0nvg5njz8v6qmqcfdq3mgg07z1cslvad958d3")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -22724,9 +24670,10 @@ Visium platform.") r-matrix r-matrixgenerics r-s4vectors + r-sparsearray r-sparsematrixstats)) (native-inputs - (list r-knitr)) + (list r-hdf5array r-knitr r-testthat)) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description @@ -22742,20 +24689,20 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "1fjc0drsdkl9cyrq5k2kskb70x63mazbhpmlk9q7v77769v64gxb")))) + "0d1n5mib93rw4x4iimz7scgxw1929m7g3cnbyfrj6iqxrp721an1")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs (list r-clue r-mass r-rcpp r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") (synopsis "Core utils for mass spectrometry data") (description @@ -22771,19 +24718,19 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "1prn45vlacj69388psimy0w05a84y8sdry6678pz611sd0ks1gka")))) + (base32 "15bligvlwhdrzmw842a4kgnzciibh8ab3aw7m73l6zaqdn4isl02")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs (list r-mscoreutils r-protgenerics r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/RforMassSpectrometry/MsFeatures") (synopsis "Functionality for mass spectrometry features") (description @@ -22801,20 +24748,20 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "0ppsldpn3vbliimjvnxadn61crck45j581dw4lc5f3w1vy5vs44h")))) + "1dqsilhlw5xwbmy04bcf6fqgnlkmzszr5xgfzhlgywdbh0pqm1lr")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-s4vectors)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/BiocIO") (synopsis "Standard input and output for Bioconductor packages") (description @@ -22834,14 +24781,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "1fzw36181rw7z62qggq7j22qhq8zrblpmv8qkqlfg140ywvwv08a")))) + "0i3ivq14jjc2v9d8v536s55w211bh67v39qzl2prringrwncq418")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -22857,14 +24804,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "0fadwss9z4bfgkhrrqv322j8x40l5cl4ib85057h4fn03qdijqhq")))) + "0pwz1hzrniqdgcxbd361w4rf5brjgb4wwz5jlny2vfnigb6v1mmd")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -22886,14 +24833,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "168yfkqlg6af8ndlw4wzb9adg4lgkgkjbsi4a435ks0n4c9dycb7")))) + "11grib7kbhjv7p2giyxhly6k3cg10p84dqdnq3fg14rda1d47xyk")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -22923,7 +24870,7 @@ relevant, and the minimum expression of the most abundant condition.") r-singlecellexperiment r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-diffcyt r-knitr r-testthat)) (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") (description @@ -22948,14 +24895,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0f4y0szdqhg63vaw7f1lmgzb72bhfpz20g9naq84s8bq2xsf8cy6")))) + "15vkr4afhszlnj4171fjj78sprgd7rcafzj2lnbrgy3r443yfn66")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -22988,14 +24935,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0g6h1h8azy79pzm0g8967f58gp33nl8866b285ybq6501nj8pb1p")))) + "1p9ja262rnvdf5gmbspkrkwvbdv4la0321m92c0l78wj3mc9y1zh")))) (build-system r-build-system) (arguments `(#:phases @@ -23036,7 +24983,7 @@ by Ernst and Kellis.") r-summarizedexperiment r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -23064,15 +25011,17 @@ interval to data view, mismatch pileup, and several splicing summaries.") (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; Tests fail with "The file does not exist". + #:tests? #false + #:phases + '(modify-phases %standard-phases ;; This is an upstream bug. (add-after 'unpack 'fix-imports (lambda _ (substitute* "NAMESPACE" ((".*maxffmode.*") "") - (("importFrom\\(ff,.*") "import(ff)\n")) - #t))))) + (("importFrom\\(ff,.*") "import(ff)\n"))))))) (propagated-inputs (list r-batchjobs r-bbmisc @@ -23088,7 +25037,7 @@ interval to data view, mismatch pileup, and several splicing summaries.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -23110,6 +25059,8 @@ and more.") "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) + ;; Tests require geuvPack, which has been removed from Bioconductor. + (arguments (list #:tests? #false)) (propagated-inputs (list r-annotationdbi r-batchjobs @@ -23142,7 +25093,7 @@ and more.") r-summarizedexperiment r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -23156,14 +25107,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "07w37kq6zx99z980if4brwmw25vjgvxd8xj3l1893idbdf70py0p")))) + "17jb2y3sgmkfs08lzb4p2l45xy8c3bfzqq653r1a6bg6rgaxviah")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -23190,7 +25141,7 @@ family of feature/genome hypotheses.") r-s4vectors r-xvector)) (native-inputs - (list r-knitr)) + (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -23205,14 +25156,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "08b70drlasws3h9d8iznaxxp0qf4n1fi943m4yngy1c65h3a30rc")))) + "1dh9av1b7df88l08y682aqmmmq5adrsh6bfc7a9rb4f6rcdzpadc")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -23228,7 +25179,7 @@ with your data.") r-snpstats r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -23239,15 +25190,17 @@ EMBL-EBI GWAS catalog.") (define-public r-gwastools (package (name "r-gwastools") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GWASTools" version)) (sha256 (base32 - "013qv2wac90s1rv992bwzq4diqfq7r18qk7gcifmi22samplpnw4")))) + "12crhc552cypi8ffl12vskrf4qw5567ag6h84ngnrmbn2k1nvjy4")))) (properties `((upstream-name . "GWASTools"))) (build-system r-build-system) + ;; TODO: This needs the package GWASdata. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biobase r-data-table r-dbi @@ -23260,7 +25213,7 @@ EMBL-EBI GWAS catalog.") r-rsqlite r-sandwich r-survival)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://github.com/smgogarten/GWASTools") (synopsis "Tools for Genome Wide Association Studies") (description @@ -23271,17 +25224,20 @@ annotation, and functions for GWAS data cleaning and analysis.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0lffqbvwmfjbw5ymxr969znvb53hbqfgq1zwffsc768rv3h4c6p7")))) + (base32 "08xk85p76dbywsxw5w0ckw31m0raar5frkz14qwz4x88ilwhrw25")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) + ;; Vignettes require connection to the internet. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-graph r-rcurl r-rgraphviz r-xml)) + (native-inputs (list r-hgu133plus2-db r-rbgl r-testthat)) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") (description @@ -23295,14 +25251,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "1l4l35bpz4j1iliy9dj09qq8r4nimd9pcm0gm4g3sb4325z6cd5h")))) + "016ly2iz42a2shfj5vm270np77cgbl92jnkjrrswk1sgghyxxi9y")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -23310,7 +25266,7 @@ functionalities including parsing, graph operation, visualization and etc.") r-matrix r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -23360,6 +25316,14 @@ on the plot.") (base32 "1sixgahjcy82yiiixgxiqbm8jcajqz0m3h0hwwm202iwzi3vyhiv")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Seven tests need INLA, which bundles mystery binaries. + (delete-file "tests/testthat/test-build_score_cache.R")))))) (inputs (list gsl)) (propagated-inputs @@ -23375,7 +25339,7 @@ on the plot.") r-rjags r-stringi)) (native-inputs - (list r-knitr)) + (list r-entropy r-knitr r-moments r-rhpcblasctl r-testthat)) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description @@ -23417,16 +25381,16 @@ other functional sequencing data.") (define-public r-parody (package (name "r-parody") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "parody" version)) (sha256 - (base32 "0k2gc8p9dk7j21n6hxdqjna09m6cggx47spkmxkqvwqm97mwqzrp")))) + (base32 "08vaqnrgkqxb99xjmgja3hs6r7n0z9chmykw6kjv6fgg914qlf2d")))) (properties `((upstream-name . "parody"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/parody") (synopsis "Parametric and resistant outlier detection") (description @@ -23438,15 +25402,17 @@ methods based on resistant statistics.") (define-public r-pathview (package (name "r-pathview") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1papw23dhhkqmm864dc3xm028xm0ywc6sjcm7xk93f2j7yj65x0v")))) + (base32 "0j7r239qvcb36025if4lqqjzxajfdjggp3cdy0h7yqziijz12kq8")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) + ;; Vignettes attempt to connect to the internet. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-annotationdbi r-graph @@ -23456,6 +25422,7 @@ methods based on resistant statistics.") r-png r-rgraphviz r-xml)) + (native-inputs (list r-runit)) (home-page "https://pathview.uncc.edu/") (synopsis "Tool set for pathway based data integration and visualization") (description @@ -23500,17 +25467,17 @@ segmented data for individual and multiple arrays.") (define-public r-snprelate (package (name "r-snprelate") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SNPRelate" version)) (sha256 (base32 - "0znk9vvnahkypmkrx82r1ryp41xr675b4ddpgx0nl3708xhncz5f")))) + "00zspm09zxp52kkivhv1pixndz7gfzb6p7rp5xvkq89qx7a9hsnn")))) (properties `((upstream-name . "SNPRelate"))) (build-system r-build-system) (propagated-inputs (list r-gdsfmt)) - (native-inputs (list r-knitr)) + (native-inputs (list r-biocgenerics r-matrix r-knitr r-runit)) (home-page "https://github.com/zhengxwen/SNPRelate") (synopsis "Toolset for relatedness and Principal Component Analysis of SNP data") @@ -23535,14 +25502,14 @@ whole-genome and whole-exome variant data.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "160pl3dy7v89i90x262hxqgipas4pyim600l6m50g3c03vm5in03")))) + "01nijl7cnzbv7pk803nv1fgqgikamlzqcah98s7051bn9xbdn2j8")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) @@ -23584,7 +25551,7 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") r-reshape2 r-rsamtools r-s4vectors)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ataudt/chromstaR") (synopsis "Chromatin state analysis for ChIP-Seq data") (description @@ -23597,14 +25564,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "1agr3n787dqly09wy274v9dg52vdb0n0z3gdh2zsbklkbmayqxqy")))) + "1hy17ajwrw1bvx6rsyxsv5h656z98ms3nj0v52xsy1ryi4iyqs49")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -23650,14 +25617,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0x3avbqf0ipmb70szf2chhbdg14ba2hwhyyz0wd66c1qwfk6aj9v")))) + "1b49hxr5glxzpcy3ykk62fcn9kqyadlhwyl01rhz70wcnryhzzd8")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -23671,7 +25638,7 @@ visualizations for publication-quality multi-panel figures.") r-s4vectors r-sva)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/ballgown") (synopsis "Flexible, isoform-level differential expression analysis") (description @@ -23684,19 +25651,23 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0394x1x81hgibvqb1dbrm8h3y72xfv9xi9fgqghjgnrw6farrkdk")))) - (properties `((upstream-name . "megadepth"))) + "1cay30y7cc6lpikcp4ncx69zjg4kyn152z5b8fhw159n6cb1z19n")))) + (properties + `((upstream-name . "megadepth") + (updater-extra-propagated-inputs . ("megadepth")))) (build-system r-build-system) - (inputs (list)) + ;; Tests attempt to install latest version of megadepth. + (arguments (list #:tests? #false)) (propagated-inputs - (list r-cmdfun + (list megadepth + r-cmdfun r-dplyr r-fs r-genomicranges @@ -23704,7 +25675,7 @@ to annotation.") r-readr r-xfun)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/LieberInstitute/megadepth") (synopsis "BigWig and BAM related utilities") (description @@ -23717,14 +25688,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "17i93h0q1fwl8wymmlgjsh8hbnaws6baf4jid5k579aap32zb5ha")))) + "06kz8433vazx7dkxysh8z9lp098irayxh23hra17bf0dih9xjcjp")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -23738,7 +25709,7 @@ regions or annotations of your choice from BigWig files.") r-rcpp r-rdpack)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/uds-helms/BEclear") (synopsis "Correction of batch effects in DNA methylation data") (description @@ -23751,15 +25722,17 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "02k83a01fb4gydnw81j2vc3d1m92y0n44bskbdrlm7cb1zscvc13")))) + "13lhps2dswd29rxr08yhpd9aqbdcvcgq5kfbymmrgr5ampl9dk29")))) (properties `((upstream-name . "BgeeCall"))) + ;; Tests need internet access. + (arguments (list #:tests? #false)) (build-system r-build-system) (propagated-inputs (list kallisto @@ -23775,7 +25748,7 @@ real numbers.") r-sjmisc r-txdbmaker r-tximport)) - (native-inputs (list r-knitr)) + (native-inputs (list r-annotationhub r-httr r-knitr r-testthat)) (home-page "https://github.com/BgeeDB/BgeeCall") (synopsis "RNA-Seq present/absent gene expression calls generation") (description @@ -23788,29 +25761,33 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "16fghmms2yb7i9rj6p3jypx6m7c3flgm8dmnkng7fvxcckaa4lry")))) + "15hnn6rk9hv623zzjsg1axydvlj3vjpwyhvhw0xpmk9q7zm6g79h")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-anndata + r-biobase + r-bread r-curl r-data-table r-digest r-dplyr r-graph + r-hdf5array r-r-utils r-rcurl r-rsqlite r-tidyr - r-topgo)) - (native-inputs (list r-knitr)) + r-topgo + r-zellkonverter)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/BgeeDB/BgeeDB_R") (synopsis "Annotation and gene expression data retrieval from Bgee database") (description @@ -23822,19 +25799,19 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0660rc8b4vkic4dbf64wkky68f0hk92ip52x7gihvv203cj9fin4")))) + "1kzlssv731qlpjrqa4l72bw2fwjzdxc5045arydnggfvcksfr2q6")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs (list r-httpuv r-httr r-jsonlite r-stringi)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/tamerh/biobtreeR") (synopsis "Use biobtree tool from R") (description @@ -23846,14 +25823,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.62.0") + (version "3.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "1627gqqk8v3sx5kgm7z3wkimbz7dpf37ljrmvwbd4z6ag2yiirbj")))) + "0laq82zi3ij8rdgv4cw6kcsbf0hrwy6v3hqr3v5x66lv8vnykp4p")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -23868,19 +25845,20 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "0jfczma8sh9dza105v306xr371f8mndndm6kw3ydgqlxd8zk3a6l")))) + "1qfakvirq5k5ypia1dfq4fwfmp9p9294bqp3s5w2a73z6ypincp2")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-ebarrays r-minet)) + (native-inputs (list r-leukemiaseset r-runit)) (home-page "https://www.cicancer.org") (synopsis "Classify diseases and build gene networks using expression profiles") (description @@ -23893,18 +25871,18 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "03958xwwywsl5ql6ss1rbkklk49ksgvbp4nqcmmqhn1hiwwn8rvi")))) + "1907n8q1y57qvrl754r888zb0vgrc0pdpvgxxki26h1x6x1y3nf8")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/dir.expiry") (synopsis "Managing expiration for cache directories") (description @@ -23917,13 +25895,13 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basic4cseq (package (name "r-basic4cseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Basic4Cseq" version)) (sha256 - (base32 "0ipxhdsqa8q49d2i17kvwyn6w2rpyl9jmq9bhch7cjawykjla5kf")))) + (base32 "0yv1j494kjkp7qgyv67j1shd0lmxsr67dsibj27ldp43p2ipyr1h")))) (properties `((upstream-name . "Basic4Cseq"))) (build-system r-build-system) (propagated-inputs @@ -23948,13 +25926,13 @@ approach and a multi-scale contact profile.") (define-public r-basics (package (name "r-basics") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BASiCS" version)) (sha256 - (base32 "0rcc8na0nravf2687bcvbaklwa0z8b43lvdy0nf9xvfrfpr1zjnw")))) + (base32 "1pdbkxamzcpgiqycp3dzmakj3laclgj3r9q9garz3q86m59fkrzb")))) (properties `((upstream-name . "BASiCS"))) (build-system r-build-system) (propagated-inputs @@ -23980,7 +25958,7 @@ approach and a multi-scale contact profile.") r-singlecellexperiment r-summarizedexperiment r-viridis)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/catavallejos/BASiCS") (synopsis "Bayesian analysis of single-cell sequencing data") (description @@ -23998,13 +25976,13 @@ pre-specified groups of cells.") (define-public r-basicstarrseq (package (name "r-basicstarrseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BasicSTARRseq" version)) (sha256 - (base32 "1w69qc81pj3c4gq158ag59wbpm2aaiqmnnb79m0h7dlsnf964cjv")))) + (base32 "0mnvrnk2p5qnrmncrkyv2ajx8wff5ax15p0z0wh8rhi3n8bhja4f")))) (properties `((upstream-name . "BasicSTARRseq"))) (build-system r-build-system) (propagated-inputs @@ -24033,20 +26011,20 @@ input.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "04amc13h4ghy1zr9wkdl42wgicxz5s2iwsspxvvi18acm06nzgfh")))) + "0vq0188f6wz0j4w0yqyki4dcp47z3d7w7m19diw7bfgy4yprqdgk")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) (propagated-inputs (list r-dir-expiry)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/basilisk.utils") (synopsis "Basilisk installation utilities") (description @@ -24057,16 +26035,18 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1jhaar524z4ly8d4c7nyjn094m4sgz4vhh8qljd2yvs30xxs0jin")))) + "0ziyxi6qcsvs2ks28vh0sdfp3xilh1kfzyhy0qwa2fwn7j7dnhr3")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) + ;; Several tests attempt to install things with Conda. + (arguments (list #:tests? #false)) (propagated-inputs (list r-basilisk-utils r-dir-expiry r-reticulate)) (native-inputs (list r-knitr)) @@ -24083,13 +26063,13 @@ Python environments in a single R session.") (define-public r-bayesknockdown (package (name "r-bayesknockdown") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BayesKnockdown" version)) (sha256 - (base32 "05plmh36s00jh4ckcgvi2s9ypa8mxlsy23mzysazbfsr022x3vqa")))) + (base32 "149ksni85zcms0kiz0as30jji9w55djzv7isnc69nd0xxp54gnyj")))) (properties `((upstream-name . "BayesKnockdown"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -24107,24 +26087,29 @@ targets. It can also be used for differential expression/2-class data.") (define-public r-bayesspace (package (name "r-bayesspace") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BayesSpace" version)) (sha256 - (base32 "0q1haqsyc61yxz1n197sv3s6csjpns4fi288kf58nnf5jgdwnyx5")))) + (base32 "08q2k2l90rjw95khlvnyz1jjlq1qyn3y5qc635nsvdlkf75fc7rz")))) (properties `((upstream-name . "BayesSpace"))) (build-system r-build-system) (propagated-inputs - (list r-assertthat + (list r-arrow + r-assertthat r-biocfilecache + r-biocparallel r-biocsingular r-coda r-dirichletreg + r-dplyr r-ggplot2 + r-magrittr r-matrix r-mclust + r-microbenchmark r-purrr r-rcpp r-rcpparmadillo @@ -24132,14 +26117,18 @@ targets. It can also be used for differential expression/2-class data.") r-rcppprogress r-rcurl r-rhdf5 + r-rjson + r-rlang r-s4vectors r-scales r-scater r-scran r-singlecellexperiment r-summarizedexperiment + r-tibble + r-tidyr r-xgboost)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://www.ezstatconsulting.com/BayesSpace/") (synopsis "Clustering and resolution enhancement of spatial transcriptomes") (description @@ -24154,13 +26143,13 @@ features such as gene expression or cell type composition can be imputed.") (define-public r-baynorm (package (name "r-baynorm") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bayNorm" version)) (sha256 - (base32 "0b05446vcqxr7smxyhmvl6rxlckzzgqhf5v1059657kihhscqr7s")))) + (base32 "1302l7j613psz19l7jshpd8aj4971qscdm7cgdr3knkfgk3dqnyz")))) (properties `((upstream-name . "bayNorm"))) (build-system r-build-system) (propagated-inputs @@ -24178,7 +26167,7 @@ features such as gene expression or cell type composition can be imputed.") r-rcppprogress r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/WT215/bayNorm") (synopsis "Single-cell RNA sequencing data normalization") (description @@ -24193,13 +26182,13 @@ posterior (3D array).") (define-public r-bbcanalyzer (package (name "r-bbcanalyzer") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BBCAnalyzer" version)) (sha256 - (base32 "16zm6fix5f5277dkdaxyxl1q1n52960ma3vw8001a5bjxhic58rn")))) + (base32 "1021srhg6j3p0lwkn3d777iylrjqm8rvspfvj73hphk8l828cd53")))) (properties `((upstream-name . "BBCAnalyzer"))) (build-system r-build-system) (propagated-inputs @@ -24223,13 +26212,13 @@ included in the plots.") (define-public r-bcrank (package (name "r-bcrank") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BCRANK" version)) (sha256 - (base32 "0ydajrbggvqakdf01pq5mqi1v3slz00irpbx4s9fmxvci9ganwp7")))) + (base32 "1fjnxv3i8mi3l5gl1c6wpph4fsn8ax08h2b25m9ihs1nxp97x682")))) (properties `((upstream-name . "BCRANK"))) (build-system r-build-system) (propagated-inputs (list r-biostrings)) @@ -24243,19 +26232,23 @@ transcription factor binding consensus by heuristic search.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1f09vw5qjxyirz5xbvnnjlwxg7z0i0y8yry49d1gyx0spyhzl7sp")))) + "0ajwp3880fr0cn647wxsd1gcyq78d2mdqwsalijh0npbr1r3zjyk")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; Tests only attempt to check R and Bioc versions. Looks like this is + ;; really only meant for actual Bioconductor infrastructure. + #:tests? #false + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs @@ -24265,7 +26258,7 @@ transcription factor binding consensus by heuristic search.") r-rlang r-styler r-usethis)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/lcolladotor/biocthis") (synopsis "Automate package and project setup for Bioconductor packages") (description @@ -24295,7 +26288,7 @@ Bioconductor-friendly.") r-memoise r-readr r-whisker)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/BiocDockerManager") (synopsis "Access and manage Bioconductor Docker images") (description @@ -24307,16 +26300,21 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "0zkd6505q0myc5l9d69i1fvfhcrjqxkv208p84zr5p7xi8jmg3dw")))) + "1mkkj2x37n5j90g5ixh6jaz5gwd0fz35wqb4s1jlp4pvxhd8jyjj")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) + ;; 83 tests fail; 1025 pass. Some of the failing tests attempt to + ;; download files and then operate on them in following tests. Since + ;; these are scattered across many files it is too messy to patch them + ;; all. + (arguments (list #:tests? #false)) (propagated-inputs (list r-biocfilecache r-chk @@ -24337,7 +26335,7 @@ the Bioconductor project.") r-withr r-xml r-yaml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/biodb") (synopsis "Library for connecting to chemical and biological databases") (description @@ -24353,19 +26351,19 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "0jys0nmp833ax96vfdh1adikpyapr5gkmldx5kvv5bqiqc8aipzb")))) + "0a0260rr13czrwfnzxmgq168jgiqd4app8rjdmywh9wg2w2xy7hf")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-matrix r-plyr r-rhdf5)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/joey711/biomformat/") (synopsis "Interface package for the BIOM file format") (description @@ -24382,14 +26380,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "1wi6acw51q48v149l72b2pp0iyjrwq1bbmr53y3m609xfadg4qim")))) + "0y96dhsqg01vcr77p7p6z5449jrg9gypqdg5raspcvz90gxivc6x")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -24402,14 +26400,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "0dfdksk3nc6pzw21sbd4cdqr05489qh4984wv0f906hyb52waxk2")))) + "0jsnycykbf2vgqfjnd7fff6k2hly7n50mavcj940vsg3gy2hfady")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -24424,14 +26422,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "1wk0qagx9s2lxykc1fp7l35kl6q17lqy6x4fl2c57v3wa11f47mi")))) + "14cvhm3r43g1b2wmjj63cfgafjbaf3zzxy0jlkp1bix4bs9fvgns")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (arguments @@ -24458,14 +26456,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "02jqlpd31mhxbvksj7ny34f6dv8skkkr76lkiaj5gm078kfr0zx5")))) + "08mhr9ichh2kynnwchmcqf4l0sn38v5sww6995jwqfyxy5vqvx4x")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -24490,7 +26488,7 @@ using aCGH or sequencing.") r-sva r-wgcna)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/almeidasilvaf/BioNERO") (synopsis "Biological network reconstruction omnibus") (description @@ -24514,14 +26512,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "0lpqvm0cx7pnb99jh7na49x10w2v04xydiwxn9l41ngxysp8v0h6")))) + "0s1mi4sjbhjs548a2bjqlj5bhslf7wzqkag80g9f2m86hxnmkxwc")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -24598,20 +26596,20 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "14yrqf5wl9r596zvlpf4y48nykg0gwzlxfgi3kdx0i5pfgvi43vk")))) + "10m1ch170d1frq6qcryiqbhb0m1nk921frw04qrxf3b4xfmgiq8c")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-edger r-rcpp)) (native-inputs - (list r-knitr)) + (list r-ineq r-knitr r-testthat)) (home-page "https://accio.github.io/BioQC/") (synopsis "Detect tissue heterogeneity in expression profiles with gene sets") (description @@ -24624,14 +26622,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.16.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1bbjfv3bi20xlk8h7r5ipav6mfs27lmj0zjb5mk1gmp071dmnk0y")))) + "0p9f9i4snkc4xgb00nwd7cky4n8s7z99lkv2lahmggk2a53bzx13")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs @@ -24654,16 +26652,18 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "06kixhzkrzxyic44kdmqrv19v2c4a7sri8cbhbvww8km4n5l39sf")))) + "06m79562baskma0vyj1632w2j669s2pymfniid5b8fyd3vqi4c6w")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) + ;; Two tests fail with "BiocParallel errors". + (arguments (list #:tests? #false)) (propagated-inputs (list r-assertthat r-biocgenerics @@ -24678,7 +26678,7 @@ help unravel disease regulatory trajectory.") r-superheat r-tibble)) (native-inputs - (list r-knitr)) + (list r-biotmledata r-knitr r-testthat)) (home-page "https://code.nimahejazi.org/biotmle/") (synopsis "Targeted learning with moderated statistics for biomarker discovery") (description @@ -24696,14 +26696,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1b7a9ryl4lz6qy2pni3k9bk6hdf147s3m7fx0icg6fkgi0ymssyx")))) + "0gxjx1x2rw07615f7p9fixf4j3ph9x9b36mcb4vwg4h0avq5wfdx")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -24731,7 +26731,7 @@ ensemble machine learning for the estimation of nuisance functions.") r-scales r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hansenlab/bsseq") (synopsis "Analyze, manage and store bisulfite sequencing data") (description @@ -24742,13 +26742,13 @@ visualizing bisulfite sequencing data.") (define-public r-dada2 (package (name "r-dada2") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dada2" version)) (sha256 (base32 - "1ac0nb5bcmzmqpi3vjdmns6xqq3ar61dks6qb3c0k48c78w88b7b")))) + "0vdvxr5s36wgkd4dry2m3ab3w4mcqhmf6y4phwg6vwmg4qrhdy0r")))) (properties `((upstream-name . "dada2"))) (build-system r-build-system) (propagated-inputs @@ -24779,14 +26779,14 @@ fragments by exact matching.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "0x7gwdzpn1ziq5vm80fs1fcyknapwjs8zfbjszw66zs36nqnqgw4")))) + "1glhz06hl5x7326lp3b8wz79vmvx855yy691cm4qzmgyxi16pdxy")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -24825,13 +26825,13 @@ interest on transformed methylation proportions.") (define-public r-omicade4 (package (name "r-omicade4") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "18gp8qpmnbc5yjqyvvwvmrdybvm6zddc0r8bfglxz5wg4a91h4wk")))) + "0c9ga5pg521w15zakwa0pw52yahj80x59lq5ziq294mj05fjmx32")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) @@ -24844,13 +26844,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.12.3") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "17a8zyvqn3avr7dwy0gr3yb8zghplyjxm1yyp5plbw91yhk8f287")))) + (base32 "14fwdckmsilq7jj1y9rg0qj0z2xrryajwhib8k8wss0ys6sk7fzz")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -24873,21 +26873,26 @@ interest on transformed methylation proportions.") r-magrittr r-progress r-purrr + r-r-utils r-rappdirs r-readr r-readxl r-rlang r-rmarkdown + r-rsqlite r-rvest r-stringi r-stringr r-tibble r-tidyr r-tidyselect + r-vctrs r-withr + r-xml r-xml2 - r-yaml)) - (native-inputs (list r-knitr)) + r-yaml + r-zip)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://saezlab.github.io/OmnipathR/") (synopsis "OmniPath web service client and more") (description @@ -24901,14 +26906,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "15bisrcgyiv9ndfvgm0p4igyr4jwsf68ccis1nf1hi9x291k7m6y")))) + "1hdfhmfgg2chsk54vrrcazi26x5adrbchmzz5wyhqi7rb85cs804")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -24940,7 +26945,7 @@ for ligand activity prediction from transcriptomics data.") r-summarizedexperiment r-variantannotation)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/trichelab/biscuiteer") (synopsis "Convenience functions for the Biscuit package") (description @@ -24953,13 +26958,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "1br2dxi5rvl8z5myrnj4dnfh8xgksrqjyy0fsqh3vjspifvis4ih")))) + (base32 "0rrk97956kyd17apjm29fxnqjhbh5mllpfr3y4yf3a3ras9chgw4")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -24986,7 +26991,7 @@ estimates, etc.") r-tidyr r-xml r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks") (synopsis "Integrative analysis with GDC data") (description @@ -25008,13 +27013,13 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "11928pcd8xzmll28m0ihi3rasc4w1i0fshn4bh9n2lyigkr5ayi4")))) + "1q9vn0gq67kkg6f4jyq05cg56qmwzl3xhiyhkgpvi1flrj9f8cpd")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs @@ -25031,7 +27036,7 @@ starburst plots) in order to easily develop complete analysis pipelines.") r-scattermore r-singlecellexperiment r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/hansenlab/tricycle") (synopsis "Transferable representation and inference of cell cycle") (description @@ -25047,14 +27052,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0lmkxl7zlp6z4i32jyy914kiwacnz89jnd2kqma81mq81r389p06")))) + "0s978mzq8pw1gj5j4j9yil0z1w5zx0msip11gkiq8wjyiipa6qg1")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs @@ -25075,7 +27080,7 @@ embeddings and functions to build new reference.") r-txdbmaker r-tximport)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/mikelove/tximeta") (synopsis "Transcript quantification import with automatic metadata") (description @@ -25089,13 +27094,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0a8q4wcqcxs7933bxg9bg03ps6hnybvcpqmlpz1pjy3affzghcbi")))) + (base32 "0s64xz2svqrdypi5nkf3yilvv66a3g6yq6321c4sk23qm6341b5n")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs @@ -25116,7 +27121,7 @@ reproducibility.") r-scales r-vegan)) (native-inputs - (list r-knitr)) + (list r-genefilter r-knitr r-testthat)) (home-page "https://github.com/joey711/phyloseq") (synopsis "Handling and analysis of high-throughput microbiome census data") (description |