diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 54 |
1 files changed, 27 insertions, 27 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 863b97463a..e2b4f6ea7f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> @@ -297,7 +297,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") `(("r-bsgenome" ,r-bsgenome) ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9))) - (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") + (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") (synopsis "Full masked genome sequences for Mouse") (description "This package provides full genome sequences for Mus musculus (Mouse) as @@ -1053,14 +1053,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.58.3") + (version "1.58.4") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "12r9ljkp3xix0xq8d1488c8wb3a4whb805v48ynmv985bs3phc71")))) + "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -1071,6 +1071,7 @@ problems in CEL-level data to help evaluate performance of quality metrics.") ("r-dbi" ,r-dbi) ("r-edger" ,r-edger) ("r-gcrma" ,r-gcrma) + ("r-glimma" ,r-glimma) ("r-ggplot2" ,r-ggplot2) ("r-gostats" ,r-gostats) ("r-gplots" ,r-gplots) @@ -1165,14 +1166,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya")))) + "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -1399,7 +1400,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.") ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-systempiper" ,r-systempiper))) - (home-page "http://bioconductor.org/packages/DiffBind") + (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description "This package computes differentially bound sites from multiple @@ -1428,7 +1429,7 @@ occupancy (overlap) analysis and plotting functions.") ("r-rsamtools" ,r-rsamtools) ("r-genomicalignments" ,r-genomicalignments) ("r-rtracklayer" ,r-rtracklayer))) - (home-page "http://bioconductor.org/packages/RIPSeeker") + (home-page "https://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") (description @@ -1457,7 +1458,7 @@ processing to visualization and annotation.") ("r-biocgenerics" ,r-biocgenerics) ("r-biobase" ,r-biobase) ("r-mass" ,r-mass))) - (home-page "http://bioconductor.org/packages/multtest") + (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description "This package can do non-parametric bootstrap and permutation @@ -1568,7 +1569,7 @@ determining dependencies between variables, code improvement suggestions.") ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-venndiagram" ,r-venndiagram))) - (home-page "http://bioconductor.org/packages/ChIPpeakAnno") + (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description "The package includes functions to retrieve the sequences around the peak, @@ -1593,7 +1594,7 @@ enrichedGO (addGeneIDs).") (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) - (home-page "http://bioconductor.org/packages/marray") + (home-page "https://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted microarray data. It also includes functions for data input, diagnostic plots, @@ -1614,7 +1615,7 @@ normalization and quality checking.") (propagated-inputs `(("r-biobase" ,r-biobase) ("r-marray" ,r-marray))) - (home-page "http://bioconductor.org/packages/CGHbase") + (home-page "https://bioconductor.org/packages/CGHbase") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by the @code{arrayCGH} packages.") @@ -1637,7 +1638,7 @@ the @code{arrayCGH} packages.") ("r-impute" ,r-impute) ("r-dnacopy" ,r-dnacopy) ("r-snowfall" ,r-snowfall))) - (home-page "http://bioconductor.org/packages/CGHcall") + (home-page "https://bioconductor.org/packages/CGHcall") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @code{arrayCGH} packages.") @@ -1666,7 +1667,7 @@ the @code{arrayCGH} packages.") ("r-matrixstats" ,r-matrixstats) ("r-r-utils" ,r-r-utils) ("r-rsamtools" ,r-rsamtools))) - (home-page "http://bioconductor.org/packages/QDNAseq") + (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, number of sequence reads in each counted, adjusted with a simultaneous @@ -1999,14 +2000,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "03cf9c94ra4f847ndlf8sn2cq1kl1055514wjq0lqbvlbfdj1dq3")))) + "1g8la7k4pnyr2hvk4yjd1bwvjy6nqbbb0fwxrrh2ifgqf4h21x2p")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -3459,14 +3460,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.14.2") + (version "3.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1y1l3yf1r1ykl9ngipvyzl5hbxxsfz7z5q5rcywkyss2b2b6gsg8")))) + "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -3492,14 +3493,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.66.0") + (version "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1vnzqd3y3jk1wgxybckzrcgwk0ly7zgcz5ki1ib0bk1jwv6xk5x8")))) + "1wc280iw9vllg6f58vsdj895yaqs8w42kl7jk8sgii009gwlaj8d")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -3517,7 +3518,6 @@ profiles (GO and KEGG) of gene and gene clusters.") ("r-mlbench" ,r-mlbench) ("r-pls" ,r-pls) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rda" ,r-rda) ("r-rpart" ,r-rpart) ("r-sfsmisc" ,r-sfsmisc) ("r-shiny" ,r-shiny) @@ -5164,14 +5164,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.18.0") + (version "1.18.6") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "05w1zrq92w3jfwq5sdyj27m5qjg4zv7acywia8vd6y5fbgcnyzlp")))) + "1sm2fmygrra9gdcs90lmk5y1ag6arga6159kggx4ij8bkhyc66vb")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5586,14 +5586,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "3.34.0") + (version "3.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762")))) + "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -6451,14 +6451,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8")))) + "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) |