diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 3021 |
1 files changed, 1737 insertions, 1284 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 27ece61f2a..1a50b78dd8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> -;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2017, 2022, 2024 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> @@ -34,6 +34,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix gexp) + #:use-module (guix utils) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) @@ -201,14 +202,14 @@ utilize the TFBSTools package (version 1.23.1 or higher).") (define-public r-mafh5-gnomad-v3-1-2-grch38 (package (name "r-mafh5-gnomad-v3-1-2-grch38") - (version "3.15.0") + (version "3.15.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MafH5.gnomAD.v3.1.2.GRCh38" version 'annotation)) (sha256 - (base32 "18hzw7f41ii16qpm3ch516b773900l1m1id5z6a763m01fg0mhiq")))) + (base32 "1q9hlva814sjfz8vm9bzw7xzppbcfy5qq7nnz9w742yr59cjb6mp")))) (properties `((upstream-name . "MafH5.gnomAD.v3.1.2.GRCh38"))) (build-system r-build-system) (propagated-inputs (list r-bsgenome @@ -290,13 +291,13 @@ even help to identify disease associations that are not obvious.") (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) (sha256 - (base32 "12lqv06n49lwczv5l4h5h6lbfbcqyg9j4csffcdx495scmhc06mc")))) + (base32 "1af2yrbpn58z34jq39qmmwprzsffgxbrs84dsxny4rksa8k6j70s")))) (properties `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) @@ -317,7 +318,7 @@ analysis.") (define-public r-org-bt-eg-db (package (name "r-org-bt-eg-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) @@ -327,7 +328,7 @@ analysis.") 'annotation)) (sha256 (base32 - "0fgrpjfrsw837ay9cq3wd6gp6sxvwjc7r9spfs4m89vqs2xb0bfc")))) + "0rbbjv47fadc6jgpqrimsd91f35fw6sw8d805vf61nx5xhbl3lpc")))) (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs @@ -342,14 +343,14 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-sc-sgd-db (package (name "r-org-sc-sgd-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Sc.sgd.db" version 'annotation)) (sha256 - (base32 "15ngfqimrjpn2fxzngj5m3pvqivbq65010qdx33xs32ax48z6p2r")))) + (base32 "1sbjwyf0ibivdhhxsaljgqa4lqp3hcf8gcrlcm2vd78bfm5cm7bg")))) (properties `((upstream-name . "org.Sc.sgd.db"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi)) @@ -391,14 +392,14 @@ Mapping50K_Xba240 (pd.mapping50k.xba240).") (define-public r-reactome-db (package (name "r-reactome-db") - (version "1.86.2") + (version "1.88.0") (source (origin (method url-fetch) (uri (bioconductor-uri "reactome.db" version 'annotation)) (sha256 (base32 - "02p8ihds0hpcfj5mib0ifql9404svlavfyj36c15jzmbci0rnc8c")))) + "1fwbf53vklhvqa6n6pijb8xqyv2pap1hskkirnm5c42wmd6g4ql7")))) (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs @@ -764,13 +765,13 @@ in Biostrings objects.") (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") - (version "1.2.11") + (version "1.2.12") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation)) (sha256 (base32 - "1hkvcrp4a2g3yl1h4k5zzj5fhp3d9a1amyn19zr62q9fhj3y47ri")))) + "0md3jl5bz4d2wkvf4yra7rydf5dgykrijrdqwwxc7f77l30nsmgp")))) (properties `((upstream-name . "GenomeInfoDbData"))) (build-system r-build-system) @@ -783,13 +784,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-go-db (package (name "r-go-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GO.db" version 'annotation)) (sha256 (base32 - "0znqa724jvrw2xx696n48lx83kzhivfr7fc9awzgm7nigwg3907m")))) + "199vk4y069yik7fn25pp73nkhs1vaw9km9rcmm1cirncwm2n0vhg")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) @@ -954,13 +955,13 @@ data.") (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) (sha256 (base32 - "1fsbrbby6ka2xdsbp8b10nid99w6lkvb7pyn8gv3dsn8p9p6mc5q")))) + "0vg6nw4qzj8janmkv6k2z471m3l4xnd1h232h0w5i53b20c7p6ys")))) (properties `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) @@ -976,13 +977,13 @@ 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 "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) (sha256 (base32 - "1n0rwynw3nl4js104295kff0jk8jwymjk8imm9di6dy6b9s3qsa6")))) + "1sqw38z73sgq66x8qrb5xw0jxyimy7l1hs2iwm7xq9ylzrjw3yj0")))) (properties `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) @@ -998,13 +999,13 @@ 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 "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) (sha256 (base32 - "1kk5jgbzcqhgwf5p4mpxswqhr9rkirm3fb7maflk61zcn6fs56zc")))) + "041hp3xhkiwh8vb4zq5kwvrsmp8paqlri6gaj1qy0a5zjlkw0fl6")))) (properties `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) @@ -1020,13 +1021,13 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) (sha256 (base32 - "1jn556ql6xknfd34qz4bqh6bgc9rccmz6pk41p7ivlzlslz7bp21")))) + "1xrbf0zmik1j70i6bg5wqvfwz4vcf3vgypan36r1lv6lspsfychr")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) @@ -1042,13 +1043,13 @@ on mapping using Entrez Gene identifiers.") (define-public r-org-mm-eg-db (package (name "r-org-mm-eg-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) (sha256 (base32 - "0i35dfllh8wf7b61ajf33gvclzg3znyx3cgp30vs3hm8ys3nras1")))) + "12d8lrf6bxvqzfxzdbxqmjcywy2myhwhi99kxdwpijsczxxfikj7")))) (properties `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) @@ -1171,29 +1172,29 @@ Ensembl.") (define-public r-escape (package (name "r-escape") - (version "1.12.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "escape" version)) (sha256 - (base32 "0bmin69ax7l5x3a0k9mv183277a0hl4znx02y79v2ilkgqkdm7fn")))) + (base32 "03wbrxd7kjyl3d4s418ql5fv7bmwdfyfp10jd8knr0xis7vxmz2x")))) (properties `((upstream-name . "escape"))) (build-system r-build-system) - (propagated-inputs (list r-biocparallel - r-broom - r-data-table + (propagated-inputs (list r-aucell + r-biocparallel r-dplyr + r-ggdist r-ggplot2 + r-ggpointdensity r-ggridges r-gseabase r-gsva - r-matrix r-matrixgenerics r-msigdbr r-patchwork r-reshape2 - r-rlang + r-seuratobject r-singlecellexperiment r-stringr r-summarizedexperiment @@ -1487,13 +1488,13 @@ data (chip hgu133plus2) assembled using data from public repositories.") (define-public r-pfam-db (package (name "r-pfam-db") - (version "3.18.0") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "PFAM.db" version 'annotation)) (sha256 - (base32 "15m7qfvz53jkdmx90y7rvy62myr4y3hdy414yqi0w3ch32vy78nr")))) + (base32 "0jjba22p8x4cfnihsa3gah3amdr4yrqpfm0zfr990jcjkvf94wvk")))) (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs @@ -1574,12 +1575,12 @@ All datasets are restricted to protein coding genes.") (define-public r-adductdata (package (name "r-adductdata") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductData" version 'experiment)) (sha256 - (base32 "16c79wy55p4ryglxph80dibfm1ni8c5yfk6fnmq064ihw4zwcld5")))) + (base32 "1ydd7zxag0cmw7mj38srqs4w6lbp1ic5i8s1ay6pifv14arcncrz")))) (properties `((upstream-name . "adductData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-experimenthub)) @@ -1595,12 +1596,12 @@ albumin} (HSA).") (define-public r-aneufinderdata (package (name "r-aneufinderdata") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinderData" version 'experiment)) (sha256 - (base32 "03kp8qkqy2wph7lbzawgnh83qjm31ih1jp986qwphfhkfk125wg0")))) + (base32 "1qysi874hsa4a7xz0na0cxv0sx02d3b74h77s30mfww1wsg8jy69")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/AneuFinderData/") (synopsis "Data package for @code{AneuFinder}") @@ -1611,12 +1612,12 @@ demonstration purposes in the @code{AneuFinder} package.") (define-public r-arrmdata (package (name "r-arrmdata") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmData" version 'experiment)) (sha256 - (base32 "0hlhc7kvw9n1bnbzingd1475qwivpx64sccnigdij8xdcm1mb4s7")))) + (base32 "02y44d0dappc3srl2d7lgipm6a62gvd8vivzaq4594dnmy8rvkw3")))) (properties `((upstream-name . "ARRmData"))) (build-system r-build-system) @@ -1630,14 +1631,14 @@ from Illumina 450k methylation arrays.") (define-public r-bcellviper (package (name "r-bcellviper") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bcellViper" version 'experiment)) (sha256 (base32 - "1q9ig5z03flq57nrhwnk6gdz4kamjmpwdfifwvnhac3l3f5z828h")))) + "0mx92gs9065lz0c01mzng9snalvmdb3xbsm1r3f6fnhg478da4yq")))) (properties `((upstream-name . "bcellViper"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -1653,14 +1654,14 @@ dataset for the examples in package viper.") (define-public r-bladderbatch (package (name "r-bladderbatch") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bladderbatch" version 'experiment)) (sha256 (base32 - "19dgvdbxsswy1fl68wwf4ifplppm1blzjw1dr06mz0yjq80a7rvl")))) + "00cgkpa6mb32q3xl5clkpdh5rkwx7c81rxmyh2qr0jpwpmd3gjwc")))) (properties `((upstream-name . "bladderbatch"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -1674,14 +1675,14 @@ dataset for the examples in package viper.") (define-public r-bodymaprat (package (name "r-bodymaprat") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bodymapRat" version 'experiment)) (sha256 - (base32 "1sfq6vxkb68l0q5qbnpm3fi53k4q9a890bv2ff9c6clhc42wx3h6")))) + (base32 "15kjgqq7lq94pjqg380swqrkv684kgbpkaikfxxdx4cpgx8sjzn7")))) (properties `((upstream-name . "bodymapRat"))) (build-system r-build-system) (arguments @@ -1712,13 +1713,13 @@ STAR. Data is available on @code{ExperimentHub} as a data package.") (define-public r-biscuiteerdata (package (name "r-biscuiteerdata") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteerData" version 'experiment)) (sha256 - (base32 "1wqdj1499psnf9y816k05m6h38yfsin4rwzqm1209ddxza6jbw1x")))) + (base32 "1qv2ajy312diacb3mihc3q7hrrlq48k5vd9v0g6w38cqz6gnz0as")))) (properties `((upstream-name . "biscuiteerData"))) (build-system r-build-system) @@ -1735,13 +1736,13 @@ biscuiteer.") (define-public r-breakpointrdata (package (name "r-breakpointrdata") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breakpointRdata" version 'experiment)) (sha256 (base32 - "13w9vp436akpnywhsr6kz763c2yakrvpyiplggfb6w50wi2xm5xj")))) + "1hm190ji3s451x2hchmpyzx6v4n8p1n6fdqg7cbzmj19rzsb4wha")))) (properties `((upstream-name . "breakpointRdata"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1755,14 +1756,14 @@ demonstrate functionalities of the @code{breakpointR} package.") (define-public r-breastcancervdx (package (name "r-breastcancervdx") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breastCancerVDX" version 'experiment)) (sha256 - (base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0")))) + (base32 "0mvm2a77mss85vi8x3i35d54z70advyshsmadhl6aysrzfiw5ifd")))) (properties `((upstream-name . "breastCancerVDX"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/breastCancerVDX") @@ -1775,21 +1776,29 @@ cancer study published in Wang et al. 2005 and Minn et al 2007.") (define-public r-celldex (package (name "r-celldex") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "celldex" version 'experiment)) (sha256 - (base32 "1ckjdmiw9g1wdswijy3dvamv3kqi11j8b8p9dgr1yv5q2lfjbnwl")))) + (base32 "155hnh62ra06b52xk78f111b10gm34d1djvl5w5mabvrk4vknwj6")))) (properties `((upstream-name . "celldex"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi + (list r-alabaster-base + r-alabaster-matrix + r-alabaster-se + r-annotationdbi r-annotationhub + r-dbi r-delayedarray r-delayedmatrixstats r-experimenthub + r-gypsum + r-jsonlite + r-matrix + r-rsqlite r-s4vectors r-summarizedexperiment)) (native-inputs (list r-knitr)) @@ -1804,13 +1813,13 @@ single-cell data or deconvolution of bulk RNA-seq.") (define-public r-champdata (package (name "r-champdata") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChAMPdata" version 'experiment)) (sha256 (base32 - "175vsg2bh578fdrdchcma5q3jq7cfxa8b7g8954xv6fxrwcj0ffz")))) + "0x006ilgqrf15135ivxv8qrcyhssl1w6pm1gpnna96za58l2f2rr")))) (properties `((upstream-name . "ChAMPdata"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-genomicranges)) @@ -1824,13 +1833,13 @@ and blood controls for CNA analysis.") (define-public r-chromstardata (package (name "r-chromstardata") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaRData" version 'experiment)) (sha256 - (base32 "13xrdr9xrfysh714q4p00pgvwr6ryhvd3jinfqr1gb27s7bdvsi6")))) + (base32 "0v28zg8z5b72hci7rqbvjvcgp979zxnq6xgck4baypmkj9ac5wn3")))) (properties `((upstream-name . "chromstaRData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/chromstaRData/") @@ -1843,13 +1852,13 @@ chromstaR package.") (define-public r-copyhelper (package (name "r-copyhelper") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) (sha256 - (base32 "1zfsxi65lln93fb87l6fgp7vxldb4fvnf95h91dl424xyq6qjp1h")))) + (base32 "1ijlba601wknkj6ybbnarcdw1z54f76gkdgynpry1v8jpbpvcadr")))) (properties `((upstream-name . "CopyhelpeR"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/CopyhelpeR/") @@ -1866,14 +1875,14 @@ GenomicRanges Bioconductor package.") (define-public r-flowsorted-blood-450k (package (name "r-flowsorted-blood-450k") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSorted.Blood.450k" version 'experiment)) (sha256 (base32 - "08xli4a24kkyy5q1ka0vyrpk11yfkyp0gxbs0k8khycppsq9s9sn")))) + "0lc45dg5jq0kqycpsggrhi5fa4xj1ciqrj6iw548ccjgdyy2w1xh")))) (properties `((upstream-name . "FlowSorted.Blood.450k"))) (build-system r-build-system) (propagated-inputs (list r-minfi)) @@ -1889,14 +1898,14 @@ associated with cell type.") (define-public r-flowsorted-blood-epic (package (name "r-flowsorted-blood-epic") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSorted.Blood.EPIC" version 'experiment)) (sha256 (base32 - "0vfx1kpy02640nkkkpksisznybv0xb6jkvvkwsybsggcr2rdkl89")))) + "1b0azyslk2g08i6v1vv2niw32f0zqasw85b9klw83zdy2f5dcdvh")))) (properties `((upstream-name . "FlowSorted.Blood.EPIC"))) (build-system r-build-system) (propagated-inputs @@ -1923,13 +1932,13 @@ https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.") (define-public r-genelendatabase (package (name "r-genelendatabase") - (version "1.38.0") + (version "1.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) (sha256 - (base32 "0skycixz0qbm8cs10kgrkl1ab1qh0mz8641mf5194y839m81d060")))) + (base32 "0rdd5nq34xd85r4i4b84ibih31mq99ljvgkm7zdv4gfggrdvi6gb")))) (properties `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) @@ -1945,13 +1954,13 @@ genomes and gene ID formats, largely based on the UCSC table browser.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomationData" version 'experiment)) (sha256 - (base32 "044q01dbcd34lxgwpg76yk0msvx7gpiibiqxp6fr9jswq6izrzq7")))) + (base32 "16mghhik2xzin14d7mqlwfy2dah3ccnga947z9id44vyz906wws7")))) (properties `((upstream-name . "genomationData"))) (build-system r-build-system) @@ -1971,13 +1980,13 @@ downloaded from Encode.") (define-public r-hdcytodata (package (name "r-hdcytodata") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDCytoData" version 'experiment)) (sha256 (base32 - "1048xgypsw257ihy0ysfxy5443dzhzp2rkjjvpivvrhw4dzl25ir")))) + "0pmzgp7x1zam3b7agi8mdq14qmx8nln9lnhiglax2pvg2a5n4ii4")))) (properties `((upstream-name . "HDCytoData"))) (build-system r-build-system) (arguments @@ -2012,14 +2021,14 @@ includes channel names, protein marker names, and protein marker classes.") (define-public r-illumina450probevariants-db (package (name "r-illumina450probevariants-db") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Illumina450ProbeVariants.db" version 'experiment)) (sha256 (base32 - "1h0qcdmyd22x5y5iwi1w89ppb1k3nb2awwim1lcxgdinab8km52b")))) + "1jpknhp624753rhalf81kvl02k4wj19xpncagzf85c878953vph0")))) (properties `((upstream-name . "Illumina450ProbeVariants.db"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/Illumina450ProbeVariants.db") @@ -2034,13 +2043,13 @@ European).") (define-public r-italicsdata (package (name "r-italicsdata") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICSData" version 'experiment)) (sha256 - (base32 "0fzx2qqykma2r2ds53wik4kb9a0wvybr63vf34s91731k21mgsqn")))) + (base32 "1d0awis142kgx9hi0dggl6gqg17m0awqzn8ncpqh2lwaka372dq8")))) (properties `((upstream-name . "ITALICSData"))) (build-system r-build-system) (home-page "http://bioinfo.curie.fr") @@ -2053,13 +2062,13 @@ package.") (define-public r-jaspar2016 (package (name "r-jaspar2016") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "JASPAR2016" version 'experiment)) (sha256 - (base32 "0dyx29f7jnyqcj85j2yrl8jcphi2kymx2y2mk7ws25xcahl5zzpy")))) + (base32 "09q5m71drbp64n26plr0a9bz71akcs4g7pqqyjmsmjrzi40kx7hr")))) (properties `((upstream-name . "JASPAR2016"))) (build-system r-build-system) (home-page "https://jaspar.elixir.no/") @@ -2072,14 +2081,14 @@ please use the package TFBSTools.") (define-public r-macrophage (package (name "r-macrophage") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "macrophage" version 'experiment)) (sha256 (base32 - "10d69v34fhxfy4nhw8h50j4q5kblm032cmjnparxm5gm7ksiqwxy")))) + "11ydl4srfxbcqnb42kwk783xd74231g6vgp1f0qs3hl8slc1hk1w")))) (properties `((upstream-name . "macrophage"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2092,17 +2101,65 @@ gene expression indicate a role for enhancer priming in immune response\", publi in Nature Genetics, January 2018.") (license license:gpl2+))) +;; This is available only in the devel branch of Bioconductor. +(define-public r-memes + (let ((commit "55f0df1fe65c8ead5252542fdc0da0ff2339049e") + (revision "1")) + (package + (name "r-memes") + (version (git-version "1.11.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/snystrom/memes") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mp3a610v293prmyid3w1w8fkjkppjnim60h7p9vz2884d0wdvk4")))) + (properties `((upstream-name . "memes"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings + r-cmdfun + r-dplyr + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-magrittr + r-matrixstats + r-patchwork + r-processx + r-purrr + r-readr + r-rlang + r-tibble + r-tidyr + r-universalmotif + r-usethis + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/snystrom/memes") + (synopsis + "Motif matching, comparison, and de novo discovery using the MEME Suite") + (description + "This package facilitates motif analysis using MEME Suite tools. +Memes provides data aware utilities for using GRanges objects as +entrypoints to motifanalysis, data structures for examining & editing +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-methylclockdata (package (name "r-methylclockdata") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylclockData" version 'experiment)) (sha256 - (base32 "0q4hiclws0fg03kwvbdwka024gghl1hbmmfficxfghslll78mc3y")))) + (base32 "1bwrgib7k71i4i6iq4l71n0z9adq3bg9k8j10bpi79ygn9169np5")))) (properties `((upstream-name . "methylclockData"))) (build-system r-build-system) (propagated-inputs (list r-experimenthub r-experimenthubdata)) @@ -2123,14 +2180,14 @@ with different methylation clocks.") (define-public r-mousegastrulationdata (package (name "r-mousegastrulationdata") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MouseGastrulationData" version 'experiment)) (sha256 (base32 - "0m03wrqgfhlyc0rmjjcj8b9gcc2rv644hffnff3j1bnkjg5rldi0")))) + "0adw98vym1jir1jrzaws7zrlfvls6rfl8bvkpq5sjy4crb33lxy2")))) (properties `((upstream-name . "MouseGastrulationData"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -2154,13 +2211,13 @@ timecourse of mouse gastrulation and early organogenesis.") (define-public r-minfidata (package (name "r-minfidata") - (version "0.48.0") + (version "0.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfiData" version 'experiment)) (sha256 (base32 - "12lhyv3zb8vps7v61zfm8sz4r18rpgphgy7nvdpj48dj3awdnpw8")))) + "1myxv7cqh7d1rjav9qhwqsmw3s1xh3zm34vbxwprqaqg87dg4bw0")))) (properties `((upstream-name . "minfiData"))) (build-system r-build-system) (propagated-inputs @@ -2177,13 +2234,13 @@ methylation arrays.") (define-public r-msdata (package (name "r-msdata") - (version "0.42.0") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msdata" version 'experiment)) (sha256 - (base32 "1jm1zjqzkd0vy8ww0k0y1fgs6i9vkg7ir6dyga001n170g11vfzr")))) + (base32 "0g7mlgks3nfnfipnybs7pvsnmrvmq8888g39badca8pi73q1cm25")))) (properties `((upstream-name . "msdata"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/msdata") @@ -2200,16 +2257,18 @@ files for various search engines.") (define-public r-msexperiment (package (name "r-msexperiment") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsExperiment" version)) (sha256 - (base32 "06m0i60zh3xjqmsz6dpp0il833xzdfj0fm6xbhl7kmicvfrcnyfg")))) + (base32 "0dxv3jw5aj1i73vqrp3c031pj26i7rp0q2zs4nq3x1vni349506d")))) (properties `((upstream-name . "MsExperiment"))) (build-system r-build-system) - (propagated-inputs (list r-iranges + (propagated-inputs (list r-biocgenerics + r-dbi + r-iranges r-protgenerics r-qfeatures r-s4vectors @@ -2234,14 +2293,14 @@ containers.") (define-public r-msigdb (package (name "r-msigdb") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msigdb" version 'experiment)) (sha256 (base32 - "1fzgq31n059zhlkny3rfwfnriz81q9brk14r5yx2zhizlv8jcais")))) + "080wm9sjwqhaxqx1r3kly1bi1gvkssqpsadnvabx11w493356qr0")))) (properties `((upstream-name . "msigdb"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -2266,13 +2325,13 @@ along with the gene set in the @code{GeneSet} class object.") (define-public r-pasilla (package (name "r-pasilla") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pasilla" version 'experiment)) (sha256 - (base32 "0dga4bb7qjigy1m1yp4bs4frwynjqfy3dnnylx4maai9x2zlynd0")))) + (base32 "0r5i64125qq5z4c8zliazsi68035d1bsz6ingzqdh37m8prdw1cr")))) (build-system r-build-system) (propagated-inputs (list r-dexseq)) (native-inputs (list r-knitr)) @@ -2287,13 +2346,13 @@ by Brooks et al., Genome Research 2011.") (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) (sha256 - (base32 "1nf6jsjvy3qacwz0dl5jc9h87xhj9q73b0g49c2yrxvv1dhayq0i")))) + (base32 "18p8hk2dq26pp4fvcf1m8wsvj1mn66i8nr900knl2n9vs09j70wy")))) (properties `((upstream-name . "HSMMSingleCell"))) (build-system r-build-system) @@ -2316,13 +2375,13 @@ resulting in a complete gene expression profile for each cell.") (define-public r-all (package (name "r-all") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALL" version 'experiment)) (sha256 - (base32 "1ny5xv338a91gc88a1y5rrd27iawrrlmxhkidvc7xdsbrwd4flkc")))) + (base32 "1yl8b8q8i19kx4viwinhyq9xn9d4axlfgjvm7cpf7pys4krhnrha")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs @@ -2340,13 +2399,13 @@ the form of an @code{exprSet} object.") (define-public r-affydata (package (name "r-affydata") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affydata" version 'experiment)) (sha256 - (base32 "1p9gqv8xnakwhf4sani09krlrq6qs4gr8yfjmi8g3s1zq4d32h1k")))) + (base32 "0srmrb2pf5dhjfm1l1jd06jgnah16qxillxi5zjr8vq7pgvw8x4b")))) (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs @@ -2362,13 +2421,13 @@ package @code{affy}.") (define-public r-gagedata (package (name "r-gagedata") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gageData" version 'experiment)) (sha256 - (base32 "13g8hzkh34c0my75xnxdffa1d67xvn9hn592s25m18400lgsfif0")))) + (base32 "1kbs0fz1jnx3grd9mpclbahwbp3749ipwfs8ggl9299bhjrgh9i6")))) (properties `((upstream-name . "gageData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/gageData") @@ -2388,13 +2447,13 @@ yeast are also included.") (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 - (base32 "0hr66p8l54nzfsizcxxd2njy44xnia607wvfhrgv46f3f8s95z02")))) + (base32 "1xdygjwqgy6kjjxzvsy25bckc0f8j5m42wrj1vrnwy5fp0q7y287")))) (properties `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) @@ -2421,14 +2480,14 @@ across the entire multi-'omics experiment.") (define-public r-parathyroidse (package (name "r-parathyroidse") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "parathyroidSE" version 'experiment)) (sha256 (base32 - "0lv7wlbdi05a3l4pv8x4cnc6jzqk1gb82rpmj1cv0nsq7gqhqscv")))) + "183cyn1i0i2p8npajwmbwzr2ncrrzwgpvh8adhjxzrdqkn3qdnr5")))) (properties `((upstream-name . "parathyroidSE"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -2445,14 +2504,14 @@ cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and contro (define-public r-sesamedata (package (name "r-sesamedata") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sesameData" version 'experiment)) (sha256 (base32 - "0a5xchdnlw9ixafk8p3ny58yqv74ba9j4z2sdyp990rbaqrx1gjw")))) + "05k67isysszzfkkbi811dkab0cmxnwz81p2ldcqz3gsq5qin3p1g")))) (properties `((upstream-name . "sesameData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub @@ -2479,13 +2538,13 @@ the @code{HorvathMethylChip40} (Mammal40) array.") (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment)) (sha256 - (base32 "04fmnqa95rb2lgflcg3d7kbz9jj990r9hlxwlhhzb79dv9wd1mfa")))) + (base32 "1r36f7nvvjjgkgmhha81n2iyr9k4nzy0qkkblm483rgzxav4gqa6")))) (properties `((upstream-name . "TCGAbiolinksGUI.data"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2498,14 +2557,14 @@ TCGAbiolinksGUI package.") (define-public r-tximportdata (package (name "r-tximportdata") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximportData" version 'experiment)) (sha256 (base32 - "0ksmg3gblkqzz40pzm35y6wghjmszrimdx7bxhq5jv4piqwii0hg")))) + "15wy0dhs9sbz27ii64b4i0zxlsm6v75m2f32gisdy9f6gnbgwkjg")))) (properties `((upstream-name . "tximportData"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2525,13 +2584,13 @@ and @code{Sailfish}. Alevin example output is also included.") (define-public r-abarray (package (name "r-abarray") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "0p9q2x6n6n1d4w2hfbhhj54qflc6rf1w1qm9p2zqv9fcrm3g153v")))) + "1kfqq4df55pxl7gnwf24aaryxijym4gzqfjyif28arlbjci9hlv6")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) @@ -2551,13 +2610,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "0y8j66yargvipwxg2ffcs62idk5q5r8vracfldbd1x5rgq7lf6nq")))) + "0zqb2w055x4whgl3mljarsnps6lkz90fwlx2lnirbnrgmlnalwjz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) @@ -2580,13 +2639,13 @@ ranking by fold-change and visualization.") (define-public r-adacgh2 (package (name "r-adacgh2") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADaCGH2" version)) (sha256 - (base32 "0lzgn4zqckv37jsgd1azvshblb38khrlcncm98g74qhkswqj5wx3")))) + (base32 "1j9dn0xw8mdfvi2ccm1d5j9q740wb89wqi6715n6jy3dljlc8irz")))) (properties `((upstream-name . "ADaCGH2"))) (build-system r-build-system) (arguments @@ -2605,7 +2664,6 @@ ranking by fold-change and visualization.") r-dnacopy r-ff r-glad - r-snapcgh r-tilingarray r-waveslim)) (home-page "https://github.com/rdiaz02/adacgh2") @@ -2622,13 +2680,13 @@ storing data.") (define-public r-adam (package (name "r-adam") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "0gz3mpkj1q4j7w08ylfzclpa6saxsz7wyp0cldllhxpcj9lxljs5")))) + "0z0rmpwfhd8p6c4zscviwsningsm740r3pb95cl8brasfdg1kl3v")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -2657,13 +2715,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "10m5dplkzxsxm7dxcmybihv81yflm3f7q6fmgb1dvwr8lsn1dm03")))) + "08kxkb6hgbw7l9dv1wn3jfdkc0sizqdgmjkrzpq73q7rf0p4248g")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs @@ -2705,13 +2763,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0299yyin2j8577db2w6mrxmsq68cjlzwyh7z1wvhbj0n1p75r871")))) + "0kihg0mwm2ysgnx3jg6xln7ibvgmky0x2hjbcmdqlg65znczh4b6")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs @@ -2754,13 +2812,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "0av0kji4r788cn5808g13svqpydq6xk4d2awpzpsckz7xbjyx0ya")))) + "13rrkb0vxkknvqhb8pgx8d13sxzy3w0wbkhhj5lrlc1kb1yqcfbh")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs @@ -2782,13 +2840,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "1f508sz5vsmmmvp2mcyd2l4hislg2xhnn11xxva010l3i7by8c2r")))) + "1241vpqkv4p3yarr6fsz1a7awvc4ff7q75ia3ra7vgkvg7gx9p93")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs @@ -2810,13 +2868,13 @@ expression values are known.") (define-public r-affyilm (package (name "r-affyilm") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyILM" version)) (sha256 - (base32 "1sbgc787gvcnpjhm0hv80rsms679wlvphq2ch7s28zdlaa2vz7sv")))) + (base32 "185kdrnvcp2jw0k71q0v4yk7583gwgi31h0n281x25hirixf6rm3")))) (properties `((upstream-name . "affyILM"))) (build-system r-build-system) (propagated-inputs @@ -2837,13 +2895,13 @@ concentrations on behal of the Langmuir model.") (define-public r-affylmgui (package (name "r-affylmgui") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affylmGUI" version)) (sha256 - (base32 "1431zmh9van9605lh0i96as48zih17s3cfhjw94v37rswfq09fkg")))) + (base32 "1qilkr3dcl6driah24kgz7lrzamq08qp2z03inm2m4r5yx8811wc")))) (properties `((upstream-name . "affylmGUI"))) (build-system r-build-system) (propagated-inputs @@ -2869,13 +2927,13 @@ limma packages.") (define-public r-affyplm (package (name "r-affyplm") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyPLM" version)) (sha256 - (base32 "0l7rfwj1bdkk9vd5j0zby2ijpapmd5k0s6l84zy4ld47vabxyaa6")))) + (base32 "1khknl7k45amyw58mcgw7kl511llyddw31qzwqc2l5c4j3bwnpz5")))) (properties `((upstream-name . "affyPLM"))) (build-system r-build-system) (inputs (list zlib)) @@ -2900,13 +2958,13 @@ also provided.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "0i7929cyqvbx81v1d629g53480m48cbdpxfv0k6lwjfzf4yvazhf")))) + "19lcs76jsdy5dz57rkdb8qqankpasrw2r5z4cy98q94az6582ix4")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) @@ -2925,13 +2983,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "06z74p3khw3r8dnwrpyyikq3ifcdvffxgfwcic9j8vc9s8pf921s")))) + "088r2ahqjv61wnzp7by4c5v9aivahmyfkzr7prnkk3ff8zh6pznl")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) @@ -2952,13 +3010,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "1i04hhncz9lhjp730gyknd8v7zakz1whc2a5pw3pn37h8k9mq5la")))) + "0qag99chj7n7l0wbb8ar0f58xs6883rgddkgj7jnrrlj3acrm12v")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs @@ -2986,13 +3044,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "0xbbcmnbnj7y3a1wndv6zhqhrwdpdj6207wh4n0qz794akciw84a")))) + "1mfi4xvx6ywkr7b7ma9ip6q2nsjvkri8qx48qyr98yyik7gg28d5")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") @@ -3008,13 +3066,13 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0fb670gxzl5aq6vmb5d2l04r0408gxrqs06k1a3b3pzkdbd7qxwm")))) + "0800jbfm488i6ccz48k49gpxr9sf9104cxcghgy9c4lzm5d3wfbm")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs @@ -3053,13 +3111,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "0cimi60asz5mmrq2qmnyqq9x5yg14cc67j8135x9zlklblsfyf35")))) + "1bm8rxfdgd0fx48fi70by08qr855jv6r4xcr7al2v9akv6vphws2")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs @@ -3083,13 +3141,13 @@ objects are used so that other packages could be used as well.") (define-public r-aims (package (name "r-aims") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AIMS" version)) (sha256 (base32 - "0fmzyd8vypcfadqfa8w11mxr12h4a9shgiqpi2n2y150fvhlqf6c")))) + "0ljdv1gww01yi0h9j9br8kp67k5wizr1dy0091kngjcbn0dxzmla")))) (properties `((upstream-name . "AIMS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071)) @@ -3107,13 +3165,13 @@ well as on dataset of gene expression data.") (define-public r-airpart (package (name "r-airpart") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 - "1bdlg078nlpibbn3y1cbkglhlm440crx3alzhv9k0psv6arg2kqb")))) + "05l5rgjfjln3kip72wj4ll4cgak9yz60xg6dgxxj690pxs1pw7bg")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs @@ -3151,16 +3209,189 @@ quality control functions for examining single cell allelic imbalance datasets.") (license license:gpl2))) +(define-public r-alabaster-base + (package + (name "r-alabaster-base") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "alabaster.base" version)) + (sha256 + (base32 "1id8cs3m1kpcfmk9aa957vy7svf7aam4kzyzic36rxcqmarr130h")))) + (properties `((upstream-name . "alabaster.base"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs (list r-alabaster-schemas + r-jsonlite + r-jsonvalidate + r-rcpp + r-rhdf5 + r-rhdf5lib + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alabaster.base") + (synopsis "Save Bioconductor objects to file") + (description + "This is a package for saving Bioconductor data structures into file +artifacts, and loading them back into memory. This is a more robust and +portable alternative to serialization of such objects into RDS files. Each +artifact is associated with metadata for further interpretation; downstream +applications can enrich this metadata with context-specific properties.") + (license license:expat))) + +(define-public r-alabaster-matrix + (package + (name "r-alabaster-matrix") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "alabaster.matrix" version)) + (sha256 + (base32 "00k0lylyhz6glqhd463bbmmldqhv5i7an9nw95md7x2m43c9gzyk")))) + (properties `((upstream-name . "alabaster.matrix"))) + (build-system r-build-system) + (propagated-inputs (list r-alabaster-base + r-biocgenerics + r-delayedarray + r-hdf5array + r-matrix + r-rcpp + r-rhdf5 + r-s4arrays + r-s4vectors + r-sparsearray)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alabaster.matrix") + (synopsis "Load and save artifacts from file") + (description + "This is a package for saving matrices, arrays and similar objects into +file artifacts, and loading them back into memory. This is a more portable +alternative to serialization of such objects into RDS files. Each artifact is +associated with metadata for further interpretation; downstream applications +can enrich this metadata with context-specific properties.") + (license license:expat))) + +(define-public r-alabaster-ranges + (package + (name "r-alabaster-ranges") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "alabaster.ranges" version)) + (sha256 + (base32 "0kjafvd4pc3bxnpjz0nvs07sdy65ad0hyzwq0nv7cifbzw9qajay")))) + (properties `((upstream-name . "alabaster.ranges"))) + (build-system r-build-system) + (propagated-inputs (list r-alabaster-base + r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-rhdf5 + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alabaster.ranges") + (synopsis "Load and save Ranges-related artifacts from file") + (description + "This is a package for saving @code{GenomicRanges}, @code{IRanges} and +related data structures into file artifacts, and loading them back into +memory. This is a more portable alternative to serialization of such objects +into RDS files. Each artifact is associated with metadata for further +interpretation; downstream applications can enrich this metadata with +context-specific properties.") + (license license:expat))) + +(define-public r-alabaster-sce + (package + (name "r-alabaster-sce") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "alabaster.sce" version)) + (sha256 + (base32 "1i9nmivsfrd7fbb8njmwihfx4xpj4p3h5bnlj9fvk5308bbj3qcg")))) + (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)) + (home-page "https://bioconductor.org/packages/alabaster.sce") + (synopsis "Load and save SingleCellExperiment from file") + (description + "This is a package for saving @code{SingleCellExperiment} into file +artifacts, and loading them back into memory. This is a more portable +alternative to serialization of such objects into RDS files. Each artifact is +associated with metadata for further interpretation; downstream applications +can enrich this metadata with context-specific properties.") + (license license:expat))) + +(define-public r-alabaster-schemas + (package + (name "r-alabaster-schemas") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "alabaster.schemas" version)) + (sha256 + (base32 "1cizlslxw0nhrfjsz3x90waa9w4n2v72a0cycbzvxqbbvkh3cp1l")))) + (properties `((upstream-name . "alabaster.schemas"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alabaster.schemas") + (synopsis "Schemas for the Alabaster framework") + (description + "This package stores all schemas required by various @code{alabaster.*} +packages. No computation should be performed by this package, as that is +handled by @code{alabaster.base}.") + (license license:expat))) + +(define-public r-alabaster-se + (package + (name "r-alabaster-se") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "alabaster.se" version)) + (sha256 + (base32 "15jggzbkl2v1jlng3bsqyf8sfvihn9amsbfgdygv04zh0kbx4i46")))) + (properties `((upstream-name . "alabaster.se"))) + (build-system r-build-system) + (propagated-inputs (list r-alabaster-base + r-alabaster-matrix + r-alabaster-ranges + r-biocgenerics + r-genomicranges + r-iranges + r-jsonlite + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alabaster.se") + (synopsis "Load and save SummarizedExperiments from file") + (description + "This is a package for saving @code{SummarizedExperiments} into file +artifacts, and loading them back into memory. This is a more portable +alternative to serialization of such objects into RDS files. Each artifact is +associated with metadata for further interpretation; downstream applications +can enrich this metadata with context-specific properties.") + (license license:expat))) + (define-public r-amountain (package (name "r-amountain") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "1c65vn2k3hzzymik9ia7nk32sf0hr83q27yzf561a1hgv3m67d65")))) + "1y2k1vg31siic6j98700m54sswbj6wr4dvbw2mz3hlm0nmsmpxc1")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) @@ -3178,13 +3409,13 @@ in multi-layer WGCN using a continuous optimization approach.") (define-public r-amplican (package (name "r-amplican") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "amplican" version)) (sha256 (base32 - "0xsw6226yyyl5zgmcyfim6dxj04zrpzbd1288l0hysq1s3b1yslw")))) + "1nbyivd5020kqkmk5ngpaixhdxgmqpifaxnfgq6yc2njqizgbhxy")))) (properties `((upstream-name . "amplican"))) (build-system r-build-system) (propagated-inputs @@ -3204,6 +3435,7 @@ in multi-layer WGCN using a continuous optimization approach.") r-knitr r-matrix r-matrixstats + r-pwalign r-rcpp r-rmarkdown r-s4vectors @@ -3225,13 +3457,13 @@ problems.") (define-public r-amaretto (package (name "r-amaretto") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "1h0ci2sak2x5dhcshmgk4hy53ggjvrz3kaj61m47w5fjkj0lz79s")))) + "0n3w00x1qajkg43ip3l63k2qs0d1x2zv8wv4xj0iqwl6r6cqgxnf")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs @@ -3277,13 +3509,13 @@ canonical cancer pathways.") (define-public r-anaquin (package (name "r-anaquin") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "1f2xf1i9l1s7433mvqjsralpm77qg0m73dw1rq9jsxbpk1f502ld")))) + "0hfvwzkfy6bm2ffghax5b228k2l6wf8zq82q13h6bxfps4wz0jgb")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs @@ -3307,13 +3539,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1m63k1b9xh5mv4zb5m9nlrdcqkh2h477x1zyfk8j89idcvk9jil7")))) + "14jdfcv3hghl1z2f7zj2mdqdyblz5sn4l1iwh8bhvih86cpigb58")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -3356,13 +3588,13 @@ these biases and construct statistically consistent estimators.") (define-public r-animalcules (package (name "r-animalcules") - (version "1.18.3") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "animalcules" version)) (sha256 (base32 - "0j8fa5cr6s20bgw7v62by61q7nk8iw64v4wshwbd2cc36gr7s3c8")))) + "1g073n8nmckd388hy9gfiddil53wv692k69ywjc85jyp5jy2n265")))) (properties `((upstream-name . "animalcules"))) (build-system r-build-system) (propagated-inputs @@ -3374,6 +3606,7 @@ these biases and construct statistically consistent estimators.") r-dplyr r-dt r-forcats + r-ggforce r-ggplot2 r-gunifrac r-lattice @@ -3391,6 +3624,7 @@ these biases and construct statistically consistent estimators.") r-shinyjs r-summarizedexperiment r-tibble + r-tidyr r-tsne r-umap r-vegan @@ -3413,13 +3647,13 @@ to understand their data better and discover new insights.") (define-public r-annotationhubdata (package (name "r-annotationhubdata") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHubData" version)) (sha256 - (base32 "09x2njf32lvj2irpjffjn2bsh42zkchirb7779xfyh745iis57mm")))) + (base32 "0wcbghjvgr8sx1qg9kyjxb7znkxhihy7jvzycrv4pyq746154xbi")))) (properties `((upstream-name . "AnnotationHubData"))) (build-system r-build-system) (arguments @@ -3464,17 +3698,18 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "1vfriymy1v3mxahfdf4sd6rawi0qy7vzxrymi852w49fmy54bgp7")))) + "0859gsgvljl2adjz4md52z4k1bcqh24i5xdfqddflw4gaq1zlm69")))) (properties `((upstream-name . "AnVIL"))) (build-system r-build-system) (propagated-inputs - (list r-biocmanager + (list r-biocbaseutils + r-biocmanager r-dplyr r-dt r-futile-logger @@ -3487,7 +3722,8 @@ for use in Bioconductor’s AnnotationHub.") r-shiny r-tibble r-tidyr - r-tidyselect)) + r-tidyselect + r-yaml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/AnVIL") (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects") @@ -3505,13 +3741,13 @@ to transform JSON responses to formats more amenable to manipulation in R.") (define-public r-aldex2 (package (name "r-aldex2") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALDEx2" version)) (sha256 (base32 - "0wchlw9dprw7vkw26h26ypx06xv2j0cxbidw61pcqaxmrrh14dhz")))) + "1bqpk93bbyajw2dm54d68f3dkc0jgcny109asfm6kcz7dg7szi3y")))) (properties `((upstream-name . "ALDEx2"))) (build-system r-build-system) (propagated-inputs @@ -3549,13 +3785,13 @@ paired or unpaired study designs.") (define-public r-alevinqc (package (name "r-alevinqc") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alevinQC" version)) (sha256 (base32 - "0lhbh9xgkbrad9fqvxl4c6y0f2kgibn6sinp8znysk5m9z0ngpwp")))) + "1pq42lvgggysg28ngxipqb1l7jfj498nxpg40h02siz6nb6inbdw")))) (properties `((upstream-name . "alevinQC"))) (build-system r-build-system) (propagated-inputs @@ -3583,13 +3819,13 @@ generated as HTML or PDF files, or as Shiny applications.") (define-public r-alphabeta (package (name "r-alphabeta") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlphaBeta" version)) (sha256 (base32 - "0zja8mysw0ljkvk6vqdx4c9wpf45zs64iyazh90mlf6xhbrvqfvq")))) + "192jyfw2676x8pgcp9h4d78283p7n6gnsdw7wzphfjn12v266fb5")))) (properties `((upstream-name . "AlphaBeta"))) (build-system r-build-system) (propagated-inputs @@ -3663,13 +3899,13 @@ data.") (define-public r-alpsnmr (package (name "r-alpsnmr") - (version "4.4.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlpsNMR" version)) (sha256 (base32 - "0141kayx20mm8skqr2210bpl76ra560ik7gf71iar03r3izcfczq")))) + "1c8ynw9424ygc4wj4drbm9gdkdqwgb5z7p72zk3x5zh3zqai0d1d")))) (properties `((upstream-name . "AlpsNMR"))) (build-system r-build-system) (propagated-inputs @@ -3717,13 +3953,13 @@ data. Efficient plotting with 1-D data is also available. Basic reading of (define-public r-altcdfenvs (package (name "r-altcdfenvs") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "altcdfenvs" version)) (sha256 (base32 - "17kgiqa5dbfp74jrm565wlx9sj4ydbds2y8ahs7dikvdvm725qsn")))) + "08k3j3dc93vg5c9ccw7mc4fri9xbdj7rdjyj0h6ig0s5866fqvlb")))) (properties `((upstream-name . "altcdfenvs"))) (build-system r-build-system) (propagated-inputs @@ -3748,13 +3984,13 @@ create an alternative mapping from sequences.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "0x7v60j1c1g12qlqxgshpmbnwzjbmlnkrfh60wl43inr0wyllq1l")))) + "0dgmg0slyrh025wgz299dzzmpirlmdhmabxspci1qfarakw5yicf")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3789,13 +4025,13 @@ sequencing data.") (define-public r-anf (package (name "r-anf") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "0yal8lbillhj3zi2rcdk7k9r748jxm3196z54y1674qxzpvp24rk")))) + "00s2rlkh5snqmvlz5a21ilmm0ngh4g362y7iayr6f78nh8gwp617")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) (propagated-inputs @@ -3817,13 +4053,13 @@ network fusion.") (define-public r-annmap (package (name "r-annmap") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "1gf0qdhj4ijgb6b67fh94zx084k5r87la3d7vc0qxs413rvr4mj8")))) + "1xijcm0c19wj2yknrlsz2ifm097z32rc58k608482686srj0bg2i")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) (propagated-inputs @@ -3851,13 +4087,13 @@ Functions to plot gene architecture and BAM file data are also provided.") (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "14lzyq08gnm9r99xwaqh50sz0dwzhmiyyylkg239dlbw80zmv404")))) + "0p2fhxzgn877mic2yv1sgcidgm74z8hxa3hdaawgvhhvi2j6v8wa")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs @@ -3877,13 +4113,13 @@ tumor samples from healthy controls.") (define-public r-arrayexpress (package (name "r-arrayexpress") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ArrayExpress" version)) (sha256 (base32 - "0cnb6r6rqbz5qph32aa1mghr0w2rhl6znyiblj0cbkv45mx2k4jr")))) + "1ad6h0pi04r9m3nwxrn7sha837m95kwii8z6s7j4zbka9ijy2pr4")))) (properties `((upstream-name . "ArrayExpress"))) (build-system r-build-system) (propagated-inputs @@ -3904,13 +4140,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (define-public r-arrayqualitymetrics (package (name "r-arrayqualitymetrics") - (version "3.58.0") + (version "3.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayQualityMetrics" version)) (sha256 (base32 - "1k80ih7r3hf48r9rp9dl2wl8m17620dqr4fch49kdsq97hm5q5dm")))) + "04y1vbpxqhqn1vsyqmscikaxn6wshsk4krcqzf2baf9x4azbdjk1")))) (properties `((upstream-name . "arrayQualityMetrics"))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -3942,13 +4178,13 @@ supported.") (define-public r-arraymvout (package (name "r-arraymvout") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayMvout" version)) (sha256 - (base32 "0z3ksx0yigan5aiq7vsdx78khlrcdxa4yd5b46rfn83gsrjbxzhz")))) + (base32 "11v3s972nyahdswqdcab0fj9jb73vd5dnd5kfb09572y4z0hn5xw")))) (properties `((upstream-name . "arrayMvout"))) (build-system r-build-system) (arguments @@ -3978,13 +4214,13 @@ fixed Type I error rate.") (define-public r-arrayquality (package (name "r-arrayquality") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayQuality" version)) (sha256 - (base32 "1bm46zf5c1i7fd848bqajv3agl05b93xsvam7034033ypyx6bf1z")))) + (base32 "0wmczy2wdxki9pam9q6ly5clvqbl018v1ar4zkdm8algjddyc2cp")))) (properties `((upstream-name . "arrayQuality"))) (build-system r-build-system) (propagated-inputs @@ -4003,13 +4239,13 @@ quality assessment.") (define-public r-asafe (package (name "r-asafe") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASAFE" version)) (sha256 (base32 - "13pn2s59npp8lhc2sk9sa7dq8fy6jlq22c71n3rcjgxrrh690nb8")))) + "13qf4jvf0m6i46bwqxdhd4zllac370ckwnd9xh6p56r1lrgcl4sa")))) (properties `((upstream-name . "ASAFE"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -4026,13 +4262,13 @@ pairs.") (define-public r-aseb (package (name "r-aseb") - (version "1.46.3") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1da6ld3ij55l3saj05ink8i1f6gqwyrv896qh8g94dmh6vzn2xbr")))) + "1h5rgy2n7rxd72ypzwnfclw8h5hvdnac48fgbfll669z2k97dsmm")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") @@ -4053,13 +4289,13 @@ RNAs.") (define-public r-asgsca (package (name "r-asgsca") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASGSCA" version)) (sha256 (base32 - "13nk19rccrp0xl1s5gjwydpl1ayc7zc2izjrij9iz7fh2r79gn7f")))) + "0gvpb1pspm7zlllg77fbi3g6csa3cpp2lbljna2m0xfi0c5zdqvw")))) (properties `((upstream-name . "ASGSCA"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) @@ -4076,13 +4312,13 @@ model as latent variables.") (define-public r-asics (package (name "r-asics") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASICS" version)) (sha256 (base32 - "0sii6sg20l6mfm8cj8zas2dm3wq6fwcwanav6fl7wkv8msk02sxb")))) + "1lqw7xmbihx9k9nm43pix0gha4j58brm0wzqf6jmag7zrgc9i6q4")))) (properties `((upstream-name . "ASICS"))) (build-system r-build-system) (propagated-inputs @@ -4110,13 +4346,13 @@ the spectra of the library with a sparse penalty.") (define-public r-aspli (package (name "r-aspli") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASpli" version)) (sha256 (base32 - "0rj103vvff2c20r018491i71393x0idq22ri4zg3qibx2accd7jy")))) + "1br4apbc3zn06ilg8fjb8xcxaimz4h7rnx9i60ak4wnpvgzgbyh2")))) (properties `((upstream-name . "ASpli"))) (build-system r-build-system) (propagated-inputs @@ -4139,6 +4375,7 @@ the spectra of the library with a sparse penalty.") r-rsamtools r-s4vectors r-tidyr + r-txdbmaker r-upsetr)) (home-page "https://bioconductor.org/packages/ASpli") (synopsis "Analysis of alternative splicing using RNA-Seq") @@ -4158,13 +4395,13 @@ that might arise in splicing patterns.") (define-public r-assessorf (package (name "r-assessorf") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AssessORF" version)) (sha256 (base32 - "0v64d3nmvcj6bz8zplyqzslm7kz6j3y0nl316h76g094hify64lk")))) + "1gzaafsfqzy2x35i251gvkd1syif80qb08kkvgnf1i6c8d2czmps")))) (properties `((upstream-name . "AssessORF"))) (build-system r-build-system) (propagated-inputs @@ -4187,13 +4424,13 @@ start codons as the forms of evidence.") (define-public r-asset (package (name "r-asset") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASSET" version)) (sha256 (base32 - "0mm15i59vsnz8zh2d10xnab3a6kq08hwd3pzm3r12g4wcrdsxfxc")))) + "1wqsnp7w3ml7azrx72fafcfbmjg4324jaxcijpcrlrrccxl5rwp4")))) (properties `((upstream-name . "ASSET"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-rmeta)) @@ -4214,24 +4451,27 @@ variant.") (define-public r-atena (package (name "r-atena") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "1qfgy76d65hbx32fw1yf20n1vavylcafb9fgqqp02r455vk3xzng")))) + "1y2v8mi9awgfbcawpcir01qglxn0bdgj6v2dsdqp6if25cizl3sr")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-biocgenerics r-biocparallel + r-cli r-genomeinfodb r-genomicalignments + r-genomicfeatures r-genomicranges r-iranges r-matrix + r-matrixgenerics r-matrixstats r-rsamtools r-s4vectors @@ -4255,13 +4495,13 @@ transcripts in an integrated manner.") (define-public r-atsnp (package (name "r-atsnp") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atSNP" version)) (sha256 (base32 - "1nksx6al1cr6apknvrabi3gdbr7m61ms81nmkq4qykx5aysmp8mv")))) + "08pcbys8iy8wzqzzvlnwc3qw7m7cswkqa3x2x2x8m4ni1s4isd6z")))) (properties `((upstream-name . "atSNP"))) (build-system r-build-system) (propagated-inputs @@ -4288,13 +4528,13 @@ SNP-led changes in motif matches.") (define-public r-attract (package (name "r-attract") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "attract" version)) (sha256 (base32 - "0lk8gfbccrxly7gn629497sxz0mj3m9wcwdahqv1m7l6fjnf5563")))) + "08l634sk6y06y2m78vsd0ld4w3h6qvx4hk6wkqflkl9jjyqpx8jy")))) (properties `((upstream-name . "attract"))) (build-system r-build-system) (propagated-inputs @@ -4319,13 +4559,13 @@ transcriptionally-coordinated changes in gene expression.") (define-public r-awfisher (package (name "r-awfisher") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AWFisher" version)) (sha256 (base32 - "10c5qi040z2w46k7qdcd2yap11mzllllrbr0nx7gd9gfzwlx089s")))) + "0z5qs337zqqri2g3m69m85xg4x5sxnqlkbwz83vhnqfzmy9nqym0")))) (properties `((upstream-name . "AWFisher"))) (build-system r-build-system) (propagated-inputs @@ -4343,13 +4583,13 @@ meta-pattern.") (define-public r-awst (package (name "r-awst") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "awst" version)) (sha256 (base32 - "0hry7ynv69hqbwyhlsilf1f9w8yadidbn2ckm5dx9mnb5ihgkyvj")))) + "1iaakdjxrz4szl4lnjcszy47q5dsh2d7i3wrr3wwdhw6wjcd62hj")))) (properties `((upstream-name . "awst"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -4370,16 +4610,16 @@ artifacts.") (define-public r-baalchip (package (name "r-baalchip") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaalChIP" version)) (sha256 (base32 - "0d08mp12lw4qdy7w7i474ywcy2zgv940nc44w0gbb9h9dfl22crv")))) + "1xm6czgbfz2rjrz5996d0n7xmlh9pd1mw9i8ac66pmn5fi44pbz2")))) (properties `((upstream-name . "BaalChIP"))) (build-system r-build-system) - (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl + (inputs (list)) ; extra/get.overlaps.v2_chrXY.perl (propagated-inputs (list r-coda r-doby @@ -4410,13 +4650,13 @@ alleles, a known phenotypical feature of cancer samples.") (define-public r-bags (package (name "r-bags") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BAGS" version)) (sha256 - (base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh")))) + (base32 "1xc7gp5fljqz26lj8sjcilm01g636p4wlzy4pzy5wgqxgfcw3zps")))) (properties `((upstream-name . "BAGS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-breastcancervdx)) @@ -4431,13 +4671,13 @@ interest.") (define-public r-basespacer (package (name "r-basespacer") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaseSpaceR" version)) (sha256 (base32 - "1ldsgrhxb1nm8xj7mws461apjknp9c2bhq3738f63i2qj9g25j4g")))) + "02f2l42p08xags155qydz97ipg5vya0prmrlw4kvahgbq5p0xm44")))) (properties `((upstream-name . "BaseSpaceR"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) @@ -4478,13 +4718,13 @@ you will have to normalize your data beforehand.") (define-public r-bader (package (name "r-bader") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BADER" version)) (sha256 (base32 - "0zmf7a7lwsnk9gcg48vmzdvfmzhvnbawwg77pb4gy3cw9sjdz5ym")))) + "15lsvfmp4qsrv12bcrz5q8yz8xyg9rckrcflr3k6si03z2vw812p")))) (properties `((upstream-name . "BADER"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BADER") @@ -4502,13 +4742,13 @@ can be used for further down-stream analyses such as gene set enrichment.") (define-public r-badregionfinder (package (name "r-badregionfinder") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BadRegionFinder" version)) (sha256 (base32 - "17smlghl8s667n6cjx64mqli9drmv0pkq51mhjlyjy2v019im7l9")))) + "1hs1mv8gj4w0wk6sw6r08j237vw3lhjrv9zip5nk6l1g1r0pg597")))) (properties `((upstream-name . "BadRegionFinder"))) (build-system r-build-system) (propagated-inputs @@ -4529,13 +4769,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.4.1") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0j2ivn93dpn7xas0bzfxhwmqzxzscgc3sjkx85y5v2ra1i6jy5k7")))) + "1pn6a74nvcpn0xzfb8167hbc6pdma0ybhh7kjpqdl4hgjp446w5w")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -4572,13 +4812,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "0y81m37c5irpaw9pfm5b672wk804n4x1g9g5pfh1dp7pggfwbf1z")))) + "1iizs0bvs7rbkwv3vs6xk26jy222kql80fp6cki0qs9h9igpzk5h")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -4610,13 +4850,13 @@ the posterior densities for the average relative abundance of transcripts.") (define-public r-banocc (package (name "r-banocc") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "banocc" version)) (sha256 (base32 - "0y6mizkbx3s2x6465g53q87q0sixxrxhjvjmvwiilhirxf4x7hgp")))) + "12fysw9m3rrmyfq1j97rdklaln6vgjdmz7hj85vrh10haz9j23s2")))) (properties `((upstream-name . "banocc"))) (build-system r-build-system) (propagated-inputs @@ -4638,13 +4878,13 @@ estimates for each correlation element.") (define-public r-barcodetrackr (package (name "r-barcodetrackr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 - "1w5p6dqagf3g27ymqsxdim0qhnwm11rrs3nnpp4mj8jcxm8wjsh9")))) + "0x0fpa44lyww2l1rdc35pdlgczz4y1vxjbn0s1frlpaacmqcxrly")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs @@ -4680,14 +4920,14 @@ retrieval analyses, or similar technologies.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.18.1") + (version "3.19.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "15wr651ylbx3am213dsy5kdr1xc8r5c9rfq5ydxzqlmxzjgymj55")))) + "1zhm28313gsbscfhfdbqizvb5v67n4l0dapjmb1xq010ikly95mh")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -4700,13 +4940,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.48.1") + (version "0.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0av525j9l0y3kjdy5wl6s35sh4nsabmdclq3687l5258kmq2dq8k")))) + "0500ya3df53xx1dfdmk50bh30ja28y6qkdwds1c1m4c7q0h2xmqi")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -4720,13 +4960,13 @@ packages.") (define-public r-breakpointr (package (name "r-breakpointr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breakpointR" version)) (sha256 (base32 - "1jhgimybc2ib201k6vs5nfyi1whpkkzn7nj562yhz74208fx793a")))) + "0imbsqrslclvfyvc00sv6ngvl5hqlr6ian07v521m63ffpx6ll78")))) (properties `((upstream-name . "breakpointR"))) (build-system r-build-system) (propagated-inputs @@ -4754,13 +4994,13 @@ export of Strand-seq data.") (define-public r-cardelino (package (name "r-cardelino") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cardelino" version)) (sha256 (base32 - "0y4d3db01jwahz01hx3dswc4gg0x5k7325v4n1illgw3ddj2mvgn")))) + "16mczwh41gf7ikbzxvggai7a8d64fn2k7q9w1yxf0sn6cwg3l0di")))) (properties `((upstream-name . "cardelino"))) (build-system r-build-system) (propagated-inputs (list r-combinat @@ -4792,13 +5032,13 @@ stochastic dropout events as well as systematic allelic imbalance is used.") (define-public r-cellid (package (name "r-cellid") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CelliD" version)) (sha256 (base32 - "13hwxhdp268h3n8d8wgr75i60apa9mama9bg049yz7c6mj5ixd1v")))) + "0c7hls5qasjd5ahrqxp2mpd402jc12pi0pgy7spcbp1fkqm8qvbl")))) (properties `((upstream-name . "CelliD"))) (build-system r-build-system) (propagated-inputs @@ -4838,13 +5078,13 @@ enrichment in single cell data.") (define-public r-coregx (package (name "r-coregx") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoreGx" version)) (sha256 - (base32 "16i8xq98vg8xgscwj0w9bsq68vjmhsvwwdw66kcphvf3jjfmn1rv")))) + (base32 "05fyncpqiq08a169rjwyc117wkyckh714z0is2r0g79920i36jas")))) (properties `((upstream-name . "CoreGx"))) (build-system r-build-system) (propagated-inputs @@ -4883,13 +5123,13 @@ the curve} or @acronym{SF, survival fraction} are included.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1sj1vr84nsbygkh5mmp7zm21zzk4zcw3bwcvcazmy54zs553blpf")))) + "1wgkn2adcxl6js3cvawhvzpxm3nmnnc16wbnzkrnsnd9l12aasih")))) (build-system r-build-system) (propagated-inputs (list r-genomicalignments @@ -4910,13 +5150,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1a5x3jzagd1a385yk1brs4say02r0l21qqjak4cl6fsv8ihhy05s")))) + "0hdm2214waz02ybr264xis48kj2anpad80jk640p49v9r17iia9l")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -4940,13 +5180,13 @@ used visualizations.") (define-public r-dama (package (name "r-dama") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "daMA" version)) (sha256 (base32 - "1ckk8h6adylaxq6bh14ym9vvrrhsfglnaigqz16v96vsj8q9i336")))) + "1hv43r6rymp09fl7vgr8jf6naixkrgl282ggf6nva0jxf1jnfmb3")))) (properties `((upstream-name . "daMA"))) (build-system r-build-system) (propagated-inputs (list r-mass)) @@ -4962,13 +5202,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "0mbm884dm30b4fwf3qr1w96j18dxdmr2bn11dw83hh0wrbhp8njm")))) + "1ffqa7a3a0f3m58j6al2hd7aa8bamv4z170y4yn1vr1f8jrb7kq5")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs @@ -5003,14 +5243,14 @@ offers nice visualization of methyl-circle plots.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1ldxw457zsfphm6izxz2kvxy3719gszhxb8mymx8njg6islljy27")))) + "0hy8cnqyvp2mrhj5wi1shh1cba79c5z8f17mfw764s2d6ivsfzz6")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -5042,13 +5282,13 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-debcam (package (name "r-debcam") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "1swqqrlwin2i2qq46qyfziblbfsfyd5hf6w39hygp7fdkpic14b7")) + "1lbgwv7009fpwqw6kl94gmm44xypn60r8kcm3fjzgbjbwijriwgq")) (snippet '(for-each delete-file '("inst/java/CornerDetect.jar" @@ -5099,7 +5339,7 @@ set analyses, and can deal with repeated or longitudinal data.") r-rjava r-summarizedexperiment)) (native-inputs - (list r-knitr zip)) + (list r-knitr zip)) ;zip is needed for repacking the jar (home-page "https://bioconductor.org/packages/debCAM") (synopsis "Deconvolution by convex analysis of mixtures") (description @@ -5116,21 +5356,16 @@ knowledge can achieve semi-supervised deconvolution of mixtures.") (define-public r-decipher (package (name "r-decipher") - (version "2.30.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "1ri8ldx3dqcpfvn3mz0022f77zi6ki04mh27qp132bbrjkj6zl79")))) + "1bgzl3sy4l5xfgxrkw8z1dvygkn2dgcl2fl9ah13ggs8hc9h9nlm")))) (build-system r-build-system) (propagated-inputs - (list r-biostrings - r-dbi - r-iranges - r-rsqlite - r-s4vectors - r-xvector)) + (list r-biostrings r-dbi r-iranges r-s4vectors r-xvector)) (home-page "https://www.bioconductor.org/packages/DECIPHER/") (synopsis "Tools for deciphering and managing biological sequences") (description "This package provides a toolset for deciphering and managing @@ -5215,13 +5450,13 @@ mechanism based on the shared signatures.") (define-public r-decomptumor2sig (package (name "r-decomptumor2sig") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decompTumor2Sig" version)) (sha256 (base32 - "13vwrg82zprb9h72azdqd0rkm5k2xm4mw7viawbzwkkqvg6azsdj")))) + "1pnxnxz9zsxqs7cbxgkjapr57k2m1d57w5hak0dwcy5zcxjzmai8")))) (properties `((upstream-name . "decompTumor2Sig"))) (build-system r-build-system) (inputs (list perl)) ;script/extractSpecColumns.pl @@ -5258,13 +5493,13 @@ of the signatures to the mutation load of the tumor.") (define-public r-deconrnaseq (package (name "r-deconrnaseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DeconRNASeq" version)) (sha256 (base32 - "1k5xrx97w9g0jfvjzawyfsqyz2fj9r463nj849djxgmcw8vp53vg")))) + "0hwvfsc48dakh3nvz60i92yciz2m5my9w57kzpyj4jyk92cs181g")))) (properties `((upstream-name . "DeconRNASeq"))) (build-system r-build-system) (propagated-inputs @@ -5285,13 +5520,13 @@ single expression profiles.") (define-public r-decontam (package (name "r-decontam") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decontam" version)) (sha256 (base32 - "0m4zd6qxsrp7w9a8psg8xcrviim6plwgwn4rgdxy8ag0c442fsvk")))) + "1xjd9jzxlj6gfd6fnygzm21q1wy5x5pl031sq1q0svq3jlnzvgb7")))) (properties `((upstream-name . "decontam"))) (build-system r-build-system) (propagated-inputs @@ -5311,13 +5546,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "0pl4nwaf8swwz9nl2ynf9mm38d0x223gpz89qrj03yihxszy2n13")))) + "181dxjj8bzy1b9xq9hd3m3ak1698w7j0sf8h9g0bhf3blzlj4pmi")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -5356,20 +5591,22 @@ make mapping WGBS data to their probe IDs easier.") (define-public r-decoupler (package (name "r-decoupler") - (version "2.8.0") + (version "2.9.7") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "1vnlrkza33nb80qf810yfz66m3j84p8chhfdxak5lvpciqwx7dh9")))) + (base32 "0zi6shh1dn8kli66dyywwgy1s809yms0jrl6lkwvzn88rms7yaqb")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs - (list r-broom + (list r-biocparallel + r-broom r-dplyr r-magrittr r-matrix + r-parallelly r-purrr r-rlang r-stringr @@ -5397,13 +5634,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "16dkjqy9ba5v8nikaxdjcz7rr60dg46sfsgrjjlp82rf3256bf8r")))) + "1rcq2bg4z6z7czqi662w5gsdc1vd4p8vb353hqayhciv31dz51fr")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -5433,13 +5670,13 @@ bases such as COSMIC.") (define-public r-degreport (package (name "r-degreport") - (version "1.38.5") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEGreport" version)) (sha256 (base32 - "0s0d40ac1da73w7j96lb20wchgs4c2svfrafsgi9mx5hiswfz25z")) + "087c7x3vz8z3yz4jdwbcskdqmv3kgz4c4vi3r9gvvay5z36yhpl5")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "DEGreport"))) @@ -5506,13 +5743,13 @@ fold changes mean and variability for each selected gene.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.28.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0mf30vdns64mpm11zcz9qx6nh5clr6krjvcmr7dqv2xg5ig0a1f7")))) + "1hjkh8xsqlfwhwxs3snpx9in58plv67aj9gsw1x8842kxfric7m7")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -5541,13 +5778,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-densvis (package (name "r-densvis") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "densvis" version)) (sha256 (base32 - "11a112r2ckzphqj3r3fxvablzwgri0j5lx3ggh1z6pfnv113xxwj")))) + "1xsafzcg6psb4ld7nk4wgdaa3xhy8i2v86asasf8h3mi1ms7lcv0")))) (properties `((upstream-name . "densvis"))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -5576,13 +5813,13 @@ heterogeneity in the original high-dimensional space.") (define-public r-derfinder (package (name "r-derfinder") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinder" version)) (sha256 (base32 - "0rj3szlpbxiwj3rajmr6ccnbs1mkcskql12iip8zgswmhz76rxh1")))) + "1i4m20wb08zncksz415jl8bd5r4gdygk7324cp6xhijrc1pfzl1i")))) (properties `((upstream-name . "derfinder"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -5622,13 +5859,13 @@ The DER Finder approach can also be used to identify differentially bounded (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "01vq8xnszxqhijranzaciapw8mcn6px0jhx9zb9lyqhsvaffjh5r")))) + (base32 "0186wjrszf6c5amibmdblabx3cfvq7p7k6kza38gahw0p7ibwv21")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs @@ -5647,17 +5884,18 @@ calculation in parallel.") (define-public r-dmrcate (package (name "r-dmrcate") - (version "2.16.1") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DMRcate" version)) (sha256 (base32 - "19dxpmjjg8v2l71yjjlfj0ycvmhi9rk04q59nwjcp0aw8nvk6l3w")))) + "1s83p6chchsx68qsfzqclpl3wq6fqy2r3namr8l3rrxp9b49342i")))) (properties `((upstream-name . "DMRcate"))) (build-system r-build-system) (propagated-inputs - (list r-biomart + (list r-annotationhub + r-biomart r-bsseq r-edger r-experimenthub @@ -5687,13 +5925,13 @@ possibly confounded by SNPs and cross-hybridisation. It includes (define-public r-drimseq (package (name "r-drimseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "1nf044cfqywfnglm081xbppamva87z2j2xz0f51z8mra11apj6i6")))) + (base32 "10skx3n3r9vp1p1499ddccgabi7q3cy1dpi5pbp4ap0gff5ika5x")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs @@ -5722,13 +5960,13 @@ results.") (define-public r-dropletutils (package (name "r-dropletutils") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DropletUtils" version)) (sha256 - (base32 "0bnxk72a0ygh4nqwyjzzi79zc4md8pwk0pr6jn43in0wdk054wf6")))) + (base32 "01y88cnii02sn1jgyvvmbx8j60qbzqyznqfxzv06yi4y0xj37klg")))) (properties `((upstream-name . "DropletUtils"))) (build-system r-build-system) (propagated-inputs @@ -5795,13 +6033,13 @@ in Python.") (define-public r-dss (package (name "r-dss") - (version "2.50.1") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 - "1wjd428kz2w3n4ak13h3i1yknm03fh911jrcy2hkcip4z5cssla0")))) + "1y9xg6ic3a03xswyfvyxdhnd7ngkljc96bm5fry4ni6kpa77bkv8")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) @@ -5821,13 +6059,13 @@ Beta-Binomial distributions.") (define-public r-dyndoc (package (name "r-dyndoc") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DynDoc" version)) (sha256 (base32 - "0d2axaszy7rpi47yg4vhd1z70m53nx40znapgg5pq6ahrx7if5f1")))) + "174jfdyq7g7mvn7wvmdkf36n0n969aqsg9bwd1nk6a5nw1khm7js")))) (properties `((upstream-name . "DynDoc"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DynDoc") @@ -5840,13 +6078,13 @@ dynamic documents and vignettes.") (define-public r-bluster (package (name "r-bluster") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "16zkv567d39258syhfb215y04sq3pnfjh9pgbp5z85hcfpz4qmhc")))) + "1bj7wx2dnwbrv2gxcmqmq815vawfiqj2xy3624fjli11r8c1hywa")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs @@ -5870,13 +6108,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.37.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1bhari5ghag5f5dlrgm79hckbh0bamd9567z04qi0spnfr97wf3s")))) + "0mq8qdhi2ccfa66rygn83hpm0fsmwiahpmrh8q522yl618mkrjcs")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -5894,14 +6132,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "1d9in3hs2n91pv498715d3qi82c7xsnm42vnzgfyz096zjghgp7a")))) + "1fi89fqzzb9n2c9jchkkgy3yq2fvisjcdavh9r455vmy0xqsyyyd")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -5954,13 +6192,13 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0rhh82hrsm32bdjamfah84p7zi8fvr4shyq2rdjfxzdp9qy5rh2q")))) + "047688hrxyg2hxd1wbywxqnvxk1622xlldzana9g5hhxg9lldrk2")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -5982,13 +6220,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "1yin2jv06g3jrzadq6yjcr14jz1zzwyxipzna5csgr013dkkrl8h")))) + (base32 "0mmxyq1r4kq1igj108pr0r9215hwmyph5svx0djd460knak24y6z")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs @@ -6011,6 +6249,7 @@ possible.") r-magrittr r-pfamanalyzer r-plyr + r-pwalign r-rcolorbrewer r-rcurl r-readr @@ -6063,13 +6302,13 @@ AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).") (define-public r-italics (package (name "r-italics") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICS" version)) (sha256 - (base32 "0zk9n94nqw6vpw908ka32zppxwqkki9krzxib06y1nic3bri3w9i")))) + (base32 "06h6iqrqzlcj4hyhj1ikl9isr3ls1pph49v5n7cp87czinr0nd3s")))) (properties `((upstream-name . "ITALICS"))) (build-system r-build-system) (propagated-inputs @@ -6198,13 +6437,13 @@ mapping.") (define-public r-nebulosa (package (name "r-nebulosa") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Nebulosa" version)) (sha256 (base32 - "11wn6l27cshhb1djsgqaqr8d33j4bipy0w0gafp3fkvg7mnpnhps")))) + "0m5z6rribsrk9mzcksjh0nmpf4d0x0hn8jd80h0hj0hj8sj1ifgv")))) (properties `((upstream-name . "Nebulosa"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -6321,14 +6560,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0lsvcv7nprmsh62d0r2v44a5n915crvv1cbj9ba6fdggj7wp8zyk")))) + "19z22c1yd3rkwk7dp8q8xv16n0qv92iz00vzid3pniy7zr80cxxy")))) (build-system r-build-system) (propagated-inputs (list r-affyio @@ -6349,14 +6588,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0818mgwny9hznw7lawrvmk11nwy0wxgjnlkf083vv3js4aq31gfp")))) + "02n2v1iwkhmilv1bjfza2yrqj7rsr8v46bghajcb8wdyyaj759ib")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -6415,14 +6654,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1jxp4qacclfl07ig8dfwy5gpnsqrfqnjbci1a7znc7acqg0kv0zv")))) + "0r4pqda9pv60b867c6yi328687kyxjglk5jmcal6xnlr75nf4w0y")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -6438,14 +6677,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "0bgv8a7hf8ns472zfryf255zqdikjv08np6k6hkpvyivad25vpwy")))) + "0w138n3f68ndr0innk981vf8p5wb729m31p0d3f9qp08hmv58jfw")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -6480,14 +6719,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "01shv7936cb5yynxkdssczl752ayv2rx4qkrkddqhi5smksw13z9")))) + "156sijj9zy01p038m7yw58h1bw1ii0kd5q9kv3krh6bs67c3dv8h")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) @@ -6504,14 +6743,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "18qjdsgkmdhwv2c4sbixp7fn69sbjdipn363jnms95dksdj2xvr9")))) + "0qqc2sq331g2ml390nhjkrnldp6bi7r6xyz7rw77hnr3qpcrhqk2")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -6532,14 +6771,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "10mdlbgbvdj967bih6wpvxmy91r10p8frhgcwv8mhv4g94ardasd")))) + "1v4sq22lwrhl50whag0jil788wwvi4rpdaij03iwak93q998ls0f")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -6559,13 +6798,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1bdr303a2z03c8vc8q95a4a4a8i956vimia5yik78yddd1ig9gq3")))) + "1g2yzbx7djkk8kccbclxv953iijmjvsjsalfv1ihmmcai33979rs")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6589,13 +6828,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "0cd2vcnx0pn5wba3x5q32vddjjp7fvix7yd7jrwv07a2fkv9c4p5")))) + "1sdm85sl4d9mqbjgjh3yizcmrzgz0g4x17s25gss2f6cjwy5jp40")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -6614,14 +6853,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0dbbg0wvk1ndv20d5j80waaz0z1bsp7y2k2m17jly4ax2hc5frc9")))) + "1ikri9hb1s0jzw1wyfpwsl02hg8dw2xs703sp085sbsq3cwk9cn1")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -6646,14 +6885,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.10.1") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "12vc573gmg8bwcfa268yq7npg7mivhngx4lx16nzan56rqb475yx")))) + "1da2n13j2xysnd175zi7s6zm8yllnp0k59vygkx9id85jcldqf51")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -6665,7 +6904,6 @@ databases. Packages produced are intended to be used with AnnotationDbi.") r-curl r-dplyr r-httr - r-interactivedisplaybase r-rappdirs r-rsqlite r-s4vectors @@ -6687,14 +6925,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.32.0") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1i6rml0slfsf01a3sphyzrxp2z759psq5bv9cfy5dxx44fnav8b8")))) + "1v24b43knsjpw44zkrzv8pvxjiw12rcz9wqp4ahd88dg23j7pvwz")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -6711,14 +6949,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "1qv2gydn8awrkbhdrgxm8zxpicphqc29rwzkj3vyaa9glmnx2y34")))) + "1jq993m6b0cv3ibgjrbzyka7svb653hvi6bvqhf8ir3lgjgs23dp")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -6741,13 +6979,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0znkawzr3hgbp2dkdk30ziqa6ylbq2nf0xmz4vi089cw9763lxgg")))) + "09xnl0qq4qsd981i9srw07228lgashcvcavi8k0izdzfyk6ka7m2")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -6764,13 +7002,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.58.2") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "03hl64j7fknw4gzw9w653zzw5gdxyi7r95vxr5ksz0m3n9xdv124")))) + "0vsjldksykgs6z7afn8kbqzl489irvvzrzq75kqkhavyhxnavqkq")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -6778,11 +7016,10 @@ on Bioconductor or which replace R functions.") (list r-annotationdbi r-biocfilecache r-digest - r-httr + r-httr2 r-progress r-rappdirs r-stringr - r-xml r-xml2)) (native-inputs (list r-knitr)) @@ -6849,13 +7086,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "19h80qf0zdxfg3pkcwwywh9gg0ymv92n51qpimnw4c3w5iaszy6b")))) + "1miw26r2a8wvgnfr9sapfv6rqk219rmsyjh6v04annafxdxy15ky")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -6900,13 +7137,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.70.3") + (version "2.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1704fn4dlswy5silmw2ri4yjbibqv249cnrb5mdgiwjh7l51w725")))) + "06vh7xa6lsw7y3b3z9s5266s00balr4si3l68hh15dwcsg3md6mh")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -6929,14 +7166,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "01hli49aq1fjjgpk465znq1ki0qi7nxg71pqg18fz6nblg3ny9z5")))) + "1jbcnjjwdjy7zfy0ybgfy1y5ym7rygzkailr5bm4hnh9bn2837p7")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -6971,13 +7208,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.70.2") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "02qrqg7lfisj44gvlfn1gkhxxjqdh11q28inxggfpcda9b67j61d")))) + "1pjbkakrycvaifl7xrmri2h94zc1ap8a9d1q4c83qji3xa21cm4q")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -7003,14 +7240,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "19qyxqky1gsrjylmc2h0sndbqlk2ibrps7123gqwn19p8kg4nhf0")))) + "0paz6h8rsbqvlxxj4di8cl76aybgjr842z5gdv8xi6c2d7zwbclw")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -7096,13 +7333,13 @@ regions and to highlight copy number alterations.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "0bx85y5888w85miif73y0yd9j4kdmjn1cfck1xshnqnsrh7p3m50")))) + "00iknjk7vgj48vj1pp7l98g7nvc3x495z3jcq5nbvdiff02faj1f")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7143,14 +7380,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1fw99xnll4jwdmp49jh59zxcbp3qs2850pjdg403sv4cg1bgfdyi")))) + "1rd56knaf0ar8d0nh0mcnrrg5jy0csixig1d4abn1b64vbzrvzpz")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -7170,14 +7407,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0zzp0kci5daffpyv56advdcs05pz3nmjn07bmm7r3hwpk0nr3fcf")))) + "1ppzx850nvvdhz2xiggr43c79w0nr0vmsmmnszasd4flf3jm7v8v")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -7332,14 +7569,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1s104b9k45b7kjrk56yw2yi4gi716nkcwnpqj4vj9w17xsb5m6zp")))) + "1j7ivkxbc75hzxhl9d97w8vamrmxf6527n7841i1j9n6s7hz1cdn")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -7370,14 +7607,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1q59agaidf0nkq599iz54a253sjxzillj39za86ihfj5xws24f8w")))) + "13y3fhgvf7438yjv6qm28n8f42w4wgkklc0q229ypns1gfh54524")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -7415,13 +7652,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "1lg7c33mdnp35b15n7ydmz4wgkgls6ii3r1q699i4ifxcgxjm8pj")))) + (base32 "1iyqvang5j55s19skd44c1zsxkphn3qqbl4sjhsw1y820ylws5r1")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -7453,14 +7690,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "1rvic3acrf4qdag423f8xa6bnqrqr31vj7k4l7a5kzf1fjm359wy")))) + "0djd84vnf4skjr6m25ykqrvwa37lgs5r5aw9md81ykaqmi40szqb")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -7480,13 +7717,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "019fdjjgzh15pbp8m16g73whbjffpm4p7hwk1nz85yc2yr1381zi")))) + "15p01f3yaan9x7y6ld1kx40jnbcn6vjjm5n6ir7cicdvv4w5ln49")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -7524,14 +7761,14 @@ code{dittoColors()}.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0xvi5mynkf1n74bn2k6gxmyhp1piwzsljd37biibdfzy14r1ir08")))) + "18h9zlah21lghy1sjpnzy6lddmff8vh3raxnqi15v00za9azk8yq")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -7564,13 +7801,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.0.16") + (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0jflbh1wsszz98y0y294g69mm81fwwxfbhpi3kmdncin8bwf8ifi")))) + "1w3dp3h30jqylbkql33j5ibp9i4vp7n1x6wdd2v0kdnv82il6hqg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7590,13 +7827,13 @@ CAGE.") (define-public r-enhancedvolcano (package (name "r-enhancedvolcano") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnhancedVolcano" version)) (sha256 (base32 - "097w3957m47m03iy8xc1m7pdgm3qy0kzqbllic8pd79qglrla802")))) + "0ry5r74d6m5x15b4azw93mjrvq4fapj4rxpi9f6macz4l5l6j1j0")))) (properties `((upstream-name . "EnhancedVolcano"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrepel)) @@ -7618,13 +7855,13 @@ parameter configurations.") (define-public r-enmix (package (name "r-enmix") - (version "1.38.01") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ENmix" version)) (sha256 (base32 - "1wh9lri9dp3904c2n6562z7p9gqx39dmag55imx8zrqnayxamc03")))) + "0cafz7bw5xha0lb3g8hfnbyj17ccb12falacxzlv4zy36mr3wxl7")))) (properties `((upstream-name . "ENmix"))) (build-system r-build-system) (propagated-inputs @@ -7660,14 +7897,14 @@ visualization of Illumina DNA methylation array data.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "010fp03x1splddxmhpxlfv1i3paqgbcxm7l9z2lmm6zfixhb158a")))) + "10h3ngwq99y0d3ksf0303qjw263ard1zsawpq1pw5n9r5g7xll47")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -7705,13 +7942,13 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-epidish (package (name "r-epidish") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EpiDISH" version)) (sha256 - (base32 "170ym3y6gd1kxghz2g5ynvgi1wrxx87b568cjcvzidpqkrkg87s6")))) + (base32 "17qkm5inavfdfrim9baqxdhs3w64c6y94qadw4y5p9xsck318frq")))) (properties `((upstream-name . "EpiDISH"))) (build-system r-build-system) (propagated-inputs (list r-e1071 @@ -7736,14 +7973,14 @@ their directionality of change in Epigenome-Wide Association Studies.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "10g9mdh7nzdz2b1k5gg5hk35lpapcnbs3p3z17k15aq040lpm236")))) + "03gl7z7q90jy47q57gfbj5fkv5n8hi43jbbrl53bdyp71f26ry2d")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges @@ -7764,14 +8001,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0bm5hvy3cdcm46527w45mnnnk95qm28xzdk1m53615gh55ix4iy8")))) + "0iwdv9y5x0na38arjqacz00s7plk7aqc1h2ynhlpbyl3nz0a0kyq")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -7792,14 +8029,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.84.0") + (version "1.86.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0q80z872d3z1jy69b53qxzvmshf5zx4qssmp4gj7fwdpfxj9qqjw")))) + "0jp7jvgzb1bs0p76j9k8lhgliipjnif6bng7hdn5wi744jb5fmpr")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -7816,13 +8053,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "074d3inz8sh8xxjliisa0p99rgy6r9fg9ljaka5bf1waxwpknzpw")))) + "0bfd4322m6g7dvas214i17k8sjsf62lza9darmhiwb4r8h30qmb2")))) (build-system r-build-system) (propagated-inputs (list r-gplots r-rcolorbrewer)) @@ -7835,13 +8072,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1vbpx187m5d5g307f4jiwyy1sw4jgj1s18622y3a458ixv540zkc")))) + "1bfy46kka77q93s42hsbxpiynfkin5mh7cz3w592smw2dzkh01j4")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -7882,18 +8119,19 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.38.8") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "126qq2549h3dpjiq36709pym5bfwk6jqbz5q2sb5hl8lwm1apv8w")))) + "12w3mgrv2rrlarpxws7m647akpscrqmzdsxnzl8hdicrh7wiydcx")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) (propagated-inputs - (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl r-s4vectors)) + (list r-biocgenerics r-genomeinfodbdata r-iranges r-s4vectors + r-ucsc-utils)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomeInfoDb") @@ -7908,13 +8146,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.38.2") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0i4n735xabdhlg7w2yd31lg65s9b6w12fhzij91hbcp0hs40fvw1")))) + "15jzdjna0r9n6ybvyw52v1d9f05vdsdxff0g8q0pa584a1sd2s7s")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7941,13 +8179,13 @@ alignments.") (define-public r-genomicdatacommons (package (name "r-genomicdatacommons") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicDataCommons" version)) (sha256 (base32 - "1inikcczkhav6h6a46ix9ixkf7b1n8rf766m5hmhmx09sspzsm5w")))) + "0jg4sa1lqn028y2ympb3x4s8yr7qa8ajrwqj2hhcl8zss3sx8gr2")))) (properties `((upstream-name . "GenomicDataCommons"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -7973,30 +8211,24 @@ Commons RESTful service.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.54.4") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0g2fv4r82ql7p2allapmgs2bj4ad70c8030vzkml7ghrxsgrryp3")))) + "1r1d9g5vq5y946v2z2xgmfb31k0576nj8i0yg6xfj9y2a0a6akc5")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi - r-biobase r-biocgenerics - r-biocio - r-biomart r-biostrings r-dbi r-genomeinfodb r-genomicranges - r-httr r-iranges - r-rjson - r-rsqlite r-rtracklayer r-s4vectors r-xvector)) @@ -8018,14 +8250,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1kvys60hhb0ndjvjdanfgciq3jc42iag8r0a199gv6w5bjaxp6wm")))) + "1b0n5aqvg6jb6rpikjzxndmcjxp31h6vhr1magzalqg7jmlvcv6i")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -8053,13 +8285,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.54.1") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1vrs3r8dyhhwj0s3vwvr168s84x5hj10lnpg1xf5c2kbj26bdv0w")))) + "18z890h4mwgizwqpz0hglgd0gmvv269cccb6i4rl3x93b519i0wx")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -8080,13 +8312,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-glad (package (name "r-glad") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GLAD" version)) (sha256 (base32 - "04wyzn56crz7sa453qj07p90vvg8nwrqz54m9ms9vf9z8adpck51")))) + "01qn4v7b7b633dz01njzmg48lga861pfqnys9f0fbk9damxc6rr1")))) (properties `((upstream-name . "GLAD"))) (build-system r-build-system) (inputs (list gsl)) @@ -8104,13 +8336,13 @@ regions identified.") (define-public r-globalancova (package (name "r-globalancova") - (version "4.20.0") + (version "4.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GlobalAncova" version)) (sha256 (base32 - "0j1ma04zjsvf668idms8hx1vnw3sh5yy8fbhwscyk1qbfy708cfh")))) + "0z71a5h4y740k0hx84aavfxl1kpshm4gqs7mh6zf895i2r761bqh")))) (properties `((upstream-name . "GlobalAncova"))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -8136,13 +8368,13 @@ linear models via the extra sum of squares principle.") (define-public r-globaltest (package (name "r-globaltest") - (version "5.56.0") + (version "5.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "globaltest" version)) (sha256 (base32 - "14kcsx1gynl0fijq67qb5zvfxn4yqj8809p7535y455rd0vddp5r")))) + "1cpvs1jcp9ibis06pkbqvhhksy6cis0zynx774d0hqdbb9ljl945")))) (properties `((upstream-name . "globaltest"))) (build-system r-build-system) (propagated-inputs @@ -8160,14 +8392,14 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.") (define-public r-gostats (package (name "r-gostats") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1v10ss1gf4a3qp6hbwa2f0la9sgiwhszg4c45qd6gv0dja2v30fs")))) + "1dygsr8nlqksfpk00lk67dhj4fcpjg1x4dbl2r4sfanlk4hq76cs")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -8192,14 +8424,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1y7z3627shskwss8bzjz1xm02rv4s7cdi91v1xqdsbdayjkrh1nb")))) + "1pnd8rmpk7gm89cvrqa8qwk40dszkfkhyydxp3gl13zng9c5bq40")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -8221,13 +8453,13 @@ Enrichment Analysis} (GSEA).") (define-public r-gsva (package (name "r-gsva") - (version "1.50.2") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSVA" version)) (sha256 (base32 - "1xgp311wh7ykvnk7nh5xik1kp2b2r08vx595znmzn28fc8rz62b1")))) + "10qv2m3gq5vzrqhcw1p4sx8szwl7a0kxf5n8xxhpplkxxq0yd3cn")))) (properties `((upstream-name . "GSVA"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -8242,6 +8474,7 @@ Enrichment Analysis} (GSEA).") r-s4vectors r-singlecellexperiment r-sparsematrixstats + r-spatialexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/rcastelo/GSVA") @@ -8258,16 +8491,41 @@ CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.") (license license:gpl2+))) +(define-public r-gypsum + (package + (name "r-gypsum") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gypsum" version)) + (sha256 + (base32 "0y5qpl19zpf5w3a1jhr4wgklp73izs3jrgbfi0axz1vgzkdsjss4")))) + (properties `((upstream-name . "gypsum"))) + (build-system r-build-system) + (propagated-inputs (list r-filelock r-httr2 r-jsonlite r-paws-storage)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ArtifactDB/gypsum-R") + (synopsis "Interface to the gypsum REST API") + (description + "This package provides a client for the gypsum REST +API (https://gypsum.artifactdb.com), a cloud-based file store in the +@code{ArtifactDB} ecosystem. This package provides functions for uploads, +downloads, and various adminstrative and management tasks. Check out the +documentation at @url{https://github.com/ArtifactDB/gypsum-worker} for more +details.") + (license license:expat))) + (define-public r-harshlight (package (name "r-harshlight") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Harshlight" version)) (sha256 (base32 - "1djs95l04b3qrqcb7jkzhfmxzbsn2riyydz8p2lmilg6z9rkdqx7")))) + "1nqi2ad9hnm6j8hn8f6xp9zav6rsa5wlzb2z5fjnm9q4xbjblnjl")))) (properties `((upstream-name . "Harshlight"))) (build-system r-build-system) (propagated-inputs @@ -8288,14 +8546,14 @@ matrix to solve the memory problem.") (define-public r-hpar (package (name "r-hpar") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "19jdy0q3larl5lxjzqlnyynq9rya56fyvf1yx9pwsyag1c148z08")))) + "1qqa0p8k3h8pbbgfz9d1k08zml5i5r9iwi2xqqj1hg84n2saqkzp")))) (build-system r-build-system) (arguments (list @@ -8323,13 +8581,13 @@ the Human Protein Atlas project.") (define-public r-r3cseq (package (name "r-r3cseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "r3Cseq" version)) (sha256 - (base32 "1llkfcy13h0c973703jmpgp2n6xxfsizb9iw1wxzgkbp1v0iy268")))) + (base32 "02dc6milwymwj90x24fip8av84ik9dp69sg9g7l300kwyk0hcrb7")))) (properties `((upstream-name . "r3Cseq"))) (build-system r-build-system) (propagated-inputs @@ -8355,13 +8613,13 @@ interactions from 3C-seq assay.") (define-public r-r4rna (package (name "r-r4rna") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "R4RNA" version)) (sha256 - (base32 "1qmr1s7z2f126wkwxjpr9fvak4i7mzgvfflkycgavbdqshn1rk6l")))) + (base32 "0cpfngd11zlws756q8cnhy5451kj8hg5ckilvmhndfapkz4w93x1")))) (properties `((upstream-name . "R4RNA"))) (build-system r-build-system) (propagated-inputs (list r-biostrings)) @@ -8378,13 +8636,13 @@ with numerical methods for computing statistics for each.") (define-public r-radiogx (package (name "r-radiogx") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RadioGx" version)) (sha256 - (base32 "0ykmvva5h1y7x9bxhqqfc18car9nasy06v1jjban7dlm95dl8nmk")))) + (base32 "0ykw5hm48fh6xqxdfgmjjbqdd5hp4dmhnykg3zkmb9wrcfp4zx7f")))) (properties `((upstream-name . "RadioGx"))) (build-system r-build-system) (propagated-inputs @@ -8423,13 +8681,13 @@ fraction} are included.") (define-public r-raggedexperiment (package (name "r-raggedexperiment") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RaggedExperiment" version)) (sha256 (base32 - "07wx2icvxgrds1w7cx9pn99z6rzk2ih938j8g1laxmgx9sya74v6")))) + "1mzjc52naf6brffv6d2bak16y3ygz9lsk8yqgcfa44180bslz3xx")))) (properties `((upstream-name . "RaggedExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biocbaseutils @@ -8457,13 +8715,13 @@ rectangular dataset.") (define-public r-rdisop (package (name "r-rdisop") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rdisop" version)) (sha256 (base32 - "1jz063hsrrbrqqx8p5yknagw19hsw51arck591h95dckncxd0006")))) + "1gcg441mp6bdnzjkh4gg6zgjn4hnw5i8mdcvb1hfim4hsc7sdsxv")))) (properties `((upstream-name . "Rdisop"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -8479,14 +8737,14 @@ be calculated to search in MS peak lists.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "2.4.1") + (version "3.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "089b5amwxwac6wvdnndy9inc218919q9dz9x58i2cp7il18vjd0c")))) + "0497b43wxcfqyr4k30f0xq7yillb4fz0gqiqxxp66gvnqv4wiv6v")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -8508,13 +8766,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-rnbeads (package (name "r-rnbeads") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RnBeads" version)) (sha256 - (base32 "15z7l4nmpy01xm19717l27nwf3rfsn6wjv211fn2y4ls40mz75qp")))) + (base32 "0v7dzmbyskq0vmja09dncg1g50dl3iycg883swb7lfvi4xzr42vj")))) (properties `((upstream-name . "RnBeads"))) (build-system r-build-system) (propagated-inputs @@ -8544,13 +8802,13 @@ methylation data at the genome scale.") (define-public r-impute (package (name "r-impute") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0q7mnx99ndna1r2r0v7jc3w8ly8qw33flwbgkcvrfhk6dzvbn4pl")))) + "1g0m9298srkhjnq3mc5rd7krr9y3cy74yvg9k0j7ypc9nmgcqabr")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -8564,13 +8822,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplay (package (name "r-interactivedisplay") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplay" version)) (sha256 (base32 - "0w81c5kc48gjavln50ysgr3vaf8s4fb6632ckzb1q225j9ik2gia")) + "14k1j8bmpbrldx61fbvn20f7l2lc50bj9iy01a5jf0ddcbi27x5g")) (snippet '(for-each delete-file '("inst/www/js/d3.v2.js" @@ -8663,14 +8921,14 @@ visualizations and interfaces for working with Bioconductor data.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "14cw90qlp8y4k0fs7xim8qvhzwbb8sn334mc72fkxg1h4bs8bxjw")))) + "0ih9b6n81gr84vhmwcq49knrbmkwbh50gy5hrap654nicb3j3jzb")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -8688,14 +8946,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "05fc1i1bcdvvy4mr4m2cdqxd3jrj1rxkxy7c43yrliv5dlikyb07")))) + "1xvi11ywr3vj2m8fpqblzg2pmj1vsc0dm8fgggv6w96l6x6sfyf0")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -8712,13 +8970,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lea (package (name "r-lea") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "LEA" version)) (sha256 (base32 - "1rhlrcp9rzf64rkabgk3gd8jqdg8ldwpkxvpfb6g49bgpkg1h6b1")))) + "0r6nj6ck77fhbmqifbx4srj1f3yr7haiinphcm0p4g8b7zn4a6fm")))) (properties `((upstream-name . "LEA"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -8743,13 +9001,13 @@ scale with the dimensions of large data sets.") (define-public r-lfa (package (name "r-lfa") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "1xrwvw7227znd1h7426k8l86197yc24b4v608issh5fqglmhljns")))) + (base32 "1sbgr6h2kpfpzw3fkqd1075wrmbblb97pdywmvl8xv52vg0wqxz3")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor r-rspectra)) @@ -8764,13 +9022,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.58.1") + (version "3.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "01byjnhhjyxk9x871rk8bgqq6lkp1a6dylqbdphpzp88b1jf2f9m")))) + "1aizqwnyk53jsbk7g9jpcyj5004yxwslrxglhamj1c55gdcr7akg")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-statmod)) @@ -8785,13 +9043,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-maaslin2 (package (name "r-maaslin2") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Maaslin2" version)) (sha256 - (base32 "1d95dv46b36ncwb7zdn0wvshg4v73qjfs3hij0jmbkkxvf2il9iq")))) + (base32 "0dl6s4lcd40nd7v0d3k3zn0mkm5rlzb8kf2cjxz298mgdif63xqh")))) (properties `((upstream-name . "Maaslin2"))) (build-system r-build-system) (propagated-inputs @@ -8833,13 +9091,13 @@ of data exploration, normalization, and transformation methods.") (define-public r-made4 (package (name "r-made4") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "03fhiszlmjh8nvz3gppf45r9kpcjrdb601ar17c4f2aygjpkf0cg")))) + "0x96lhkz0fwp3qis8k2lllmi520b887bz26jcq3zlk1kjhbg91a8")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs @@ -8862,13 +9120,13 @@ datasets (coinertia analysis).") (define-public r-makecdfenv (package (name "r-makecdfenv") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "makecdfenv" version)) (sha256 (base32 - "0mggcw0390i1y2wn4k8570gjmbsx6hbipi8fkhz2zj9icsx89x1l")))) + "0c1ks5f2rc0mwbfji6iicvypbmm46mq8yckmdpwiyp22l7l05aqz")))) (properties `((upstream-name . "makecdfenv"))) (build-system r-build-system) (inputs (list zlib)) @@ -8889,13 +9147,13 @@ package that automatically loads that environment.") (define-public r-manor (package (name "r-manor") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MANOR" version)) (sha256 - (base32 "10zf6c1vx6cp4wg6axpmbpxk2hlmf6mga7rdh765fznwb71r4h0x")))) + (base32 "0mlhv4gy4bxvdm0drwwrm4x48wy0mghzcqhvaw2rhw0h65rmy5ps")))) (properties `((upstream-name . "MANOR"))) (build-system r-build-system) (propagated-inputs (list r-glad)) @@ -8912,13 +9170,13 @@ experiments.") (define-public r-maser (package (name "r-maser") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maser" version)) (sha256 (base32 - "0h7x1fyfvnjc30w9ydbnlqijz58q2kcxv4yy784rf4adsrdhwh45")))) + "0w62dl65ysgcwixgmmb70qp6f85vhfnqjsww5snkjd48ypwx65ca")))) (properties `((upstream-name . "maser"))) (build-system r-build-system) (propagated-inputs @@ -8944,13 +9202,13 @@ and visualizaton of alternative splicing events generated by rMATS.") (define-public r-mdqc (package (name "r-mdqc") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mdqc" version)) (sha256 - (base32 "0q6ig9qdf2s9329wysrvgh13yq5c7n76as2c3mahqm78xb0mpplf")))) + (base32 "1frn6s43j6sbwnb5h2hykccvi7cwbasp8l37rc3nkxpc6szvsby6")))) (properties `((upstream-name . "mdqc"))) (build-system r-build-system) (propagated-inputs @@ -8969,16 +9227,16 @@ high distances can be flagged as potentially low-quality.") (define-public r-metabocoreutils (package (name "r-metabocoreutils") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaboCoreUtils" version)) (sha256 - (base32 "0bs24dwqlm8isp231jds51l7v16q0gjli1qmhjxyva3qmi5yb4dl")))) + (base32 "1y5lq1x60pcvxsl8dim5plzd3y4bqjkcam5hv9614xw0sr4h0r04")))) (properties `((upstream-name . "MetaboCoreUtils"))) (build-system r-build-system) - (propagated-inputs (list r-mscoreutils)) + (propagated-inputs (list r-biocparallel r-mscoreutils)) (native-inputs (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MetaboCoreUtils") (synopsis "Core utils for Metabolomics data") @@ -8995,13 +9253,13 @@ mixes commonly used in MS experiments.") (define-public r-metagenomeseq (package (name "r-metagenomeseq") - (version "1.43.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metagenomeSeq" version)) (sha256 - (base32 "1m19qkwrbfr4yhbr1izfjka3brn1qasqql6alczv55l5h52m4s4b")))) + (base32 "0bjbiwbgs0lv0j6gjv5rhqhmqk0p7f80lfig4n24i4bqwkd2j26k")))) (properties `((upstream-name . "metagenomeSeq"))) (build-system r-build-system) (propagated-inputs @@ -9029,13 +9287,13 @@ correlations.") (define-public r-metaneighbor (package (name "r-metaneighbor") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaNeighbor" version)) (sha256 (base32 - "0y8nk9jq0z48phg13mf6hsfg8l54w6z6b67g0k1c9gmsb7aqq04d")))) + "0sz15njb0y9vcmbv89k3x2sw4px8nmy3qhqkvyl69kxlcqdicgxi")))) (properties `((upstream-name . "MetaNeighbor"))) (build-system r-build-system) (propagated-inputs @@ -9065,13 +9323,13 @@ profiles than cells of different types.") (define-public r-methylaid (package (name "r-methylaid") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MethylAid" version)) (sha256 - (base32 "0mzml9j6f7yycf9747ikkpfvxnwji07h8jhwa9a54ix2d0wyxk3d")))) + (base32 "084mnllaj6qp5ai5bmj6wgc90bs270qbzl60sch1f863x8fv9lzr")))) (properties `((upstream-name . "MethylAid"))) (build-system r-build-system) (propagated-inputs @@ -9103,13 +9361,13 @@ be explored.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0y45wa45kblm2g3nylvybvyfc34sjlynhsz3dirhs1favb83sdiv")))) + "000dvi63cjikjbq3q83hlspd7y62rpswzg6hs5z1z1pj6a8rifdj")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9150,13 +9408,13 @@ TAB-Seq.") (define-public r-mfuzz (package (name "r-mfuzz") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Mfuzz" version)) (sha256 (base32 - "0v2l3fi9331lxfam6az265rfk52g4n75hh4rg12ykhp86ihplzpf")))) + "00sx63bg5qw22vw0yw3syhyl5ffjrqvf81b9ksgw2p0z3yiiss5h")))) (properties `((upstream-name . "Mfuzz"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-tkwidgets)) @@ -9170,13 +9428,13 @@ time-series data (including a graphical user interface).") (define-public r-mmuphin (package (name "r-mmuphin") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MMUPHin" version)) (sha256 - (base32 "0lhvsx5yjvqh5d3h860sv8cf3h73nrzvljpkqrd9ks0irc4gcm6d")) + (base32 "0wvsngvxik4j1bz4w32482ffczh6qj3kzghqhh8l02cbd2908z55")) ;; Delete generated files. (snippet '(for-each delete-file @@ -9238,13 +9496,13 @@ It has function interfaces for: (define-public r-modstrings (package (name "r-modstrings") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Modstrings" version)) (sha256 - (base32 "1jjawwkvdx02ss2vw4ah2b8psgxr01z6r1rkr2pnkmrp2ma7ygks")))) + (base32 "0yc8gsgxlww2g9z1m6jl02aqmama10fkr2mvibvdi01s5pqwdbky")))) (properties `((upstream-name . "Modstrings"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -9302,14 +9560,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "0vasr9rwnfjxbb3y2saq7gqzis5xyamgvns2rlywdxv1jm0nr8y3")))) + "1gafcq3p693f28gz3p8hk8mlxd9zja95h8953sr56n7krfffy1gi")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -9352,14 +9610,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "19ya4ax6pa727hdn0118l9pwa9dxgh89dz54mm66dawxga3jhar4")))) + "0smf4l023ckwsm5ckrqqw7kjyi1awp378mzhab7v8nk9n5smsj61")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -9398,13 +9656,13 @@ in SNV base substitution data.") (define-public r-msa (package (name "r-msa") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msa" version)) (sha256 (base32 - "1csa8j64xrfr6kdnndr3876bplclca9wf6ydy9kg97xsjq7gz8q5")))) + "05i6pp10nn4icl51rx3b48s861hnd1yx72d933fphm6a5082zxms")))) (properties `((upstream-name . "msa"))) (build-system r-build-system) (propagated-inputs @@ -9429,14 +9687,14 @@ package TeXshade.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.28.1") + (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1622mmm5n8yl4qjq8bda7689qdfz1rhyxyh8s3q5475al1d0mpsl")))) + "0cdvi2mjvhj0h8x2rh3kkzrdnmzhr7d9a41m21r6b843a0q7hp6f")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9457,11 +9715,11 @@ package TeXshade.") r-pcamethods r-plyr r-protgenerics + r-psmatch r-rcpp r-s4vectors r-scales - r-vsn - r-xml)) + r-vsn)) (native-inputs (list r-knitr)) (home-page "https://github.com/lgatto/MSnbase") @@ -9474,14 +9732,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1hmfh7v7p5d741x2wh1njqwkmfmf3xmwkqy88kalrcjzrdwfpv9b")))) + "0misrm4x4z5h8dfwcrwi24nhcjslqvbyk5n7qz6kf2zcgcwq8q44")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -9531,14 +9789,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1rgkd9iv0lxj1zxh96sifwa312ivw5kl5jw82ma4fmapr4iqhzsh")))) + "0kh9swzh3hvi6qi64cgr13f22s1mgvz2rid5psb1gy4l3biwadj5")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9562,14 +9820,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0z6ckp69syrdzhp6n4n399k2lar3w4n2d1ji2f90951c4ds6hkh8")) + "02dz23xns9ryz98nip1w68h9q5ckxpyl1zvzklsp4j7p9z2400dk")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) @@ -9682,14 +9940,14 @@ Gao et al in Nature Biotechnology 2022}.") (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "1s55fiqgxrdznn43qhm5yv9gp8d1msr2f39wxih0b5bm4wxhkq45")))) + "03z5pyqbaxwyrq5m858c8k69fwvclq98ksr84dc4m7r8lzz2hfxx")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs @@ -9721,14 +9979,14 @@ functionality of the @code{TxDb} packages (e.g., (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0g75y21lqmwsh28nx99zp2gxr6rhlhbw76f66qx5hrh6bm2zpm7j")))) + "1cfh632rpmklmyd5cibwiy0i2pk2kk2m39g8mq5sxfwd2am4r0jk")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -9742,7 +10000,8 @@ functionality of the @code{TxDb} packages (e.g., r-graph r-iranges r-rbgl - r-s4vectors)) + r-s4vectors + r-txdbmaker)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") @@ -9754,13 +10013,13 @@ the fact that each of these packages implements a select methods.") (define-public r-oscope (package (name "r-oscope") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Oscope" version)) (sha256 (base32 - "1li2l9mdq2q0580a7qzvfid5n15v62fr9ys87j42k3l2w5a26smf")))) + "16d2ngakdg73rdx0bf1pz3z1n8npjzl3b7dn94g9zbayw4vp3x5z")))) (properties `((upstream-name . "Oscope"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) @@ -9780,14 +10039,14 @@ insertion module to recover the base cycle order for each oscillator group.") (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "0ihc9jqjy0nl4pfgcxczfdf973nb99325agk73y0222ad1mpkc07")))) + "1szl2gyhw55ad4phcb7qn14amjb6xg65l3p4hnjzp6rda2cy9437")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs @@ -9835,14 +10094,14 @@ application encapsulates the whole analysis.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.94.0") + (version "1.96.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1asm4iafdzm98iv2j9sxvn5y9ss2p679cx7gwjipq8mf1d7bzfp0")))) + "1hrq0xmpr1l95hyi6ls9r86ahwf2rcbvr8m7cpg6ra0gsfyn4mpi")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9862,13 +10121,13 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-pfamanalyzer (package (name "r-pfamanalyzer") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pfamAnalyzeR" version)) (sha256 (base32 - "0qxxp7kfwbb9q471mgwc4bd8dmyid56ddyzw2jlg4gb1wcq9py67")))) + "06bp5nghgrj8qyzqp1v869vck1j10093r9dp67w0kav4x4srkyyl")))) (properties `((upstream-name . "pfamAnalyzeR"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble)) @@ -9885,13 +10144,13 @@ domain isotypes from pfam data.") (define-public r-piano (package (name "r-piano") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "piano" version)) (sha256 - (base32 "0rw55ig3pbvi2kyg10rx60ldcncsd4gki2h1zpr1nhmqg3fv0l5y")))) + (base32 "0v168wkwxzh70h2c08ad4dzlgklbgvx1fzwrzw2mqq0fyczj0diw")))) (properties `((upstream-name . "piano"))) (build-system r-build-system) (propagated-inputs @@ -9922,13 +10181,13 @@ set analyses.") (define-public r-polyester (package (name "r-polyester") - (version "1.38.0") + (version "1.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "polyester" version)) (sha256 - (base32 "1iycdxj0jhh2faclfzflp2cjc2zmxmhy03avv75h0qg3j5kf35l4")))) + (base32 "0fw0qhmbygjq4ryspyqikb8rxfn33ks000j7sshgfg8hf2rmqg3x")))) (properties `((upstream-name . "polyester"))) (build-system r-build-system) (propagated-inputs @@ -9950,13 +10209,13 @@ comparisons of methods for differential expression.") (define-public r-powertcr (package (name "r-powertcr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "powerTCR" version)) (sha256 - (base32 "06fmphdq95pjbbvm8m8h1wajbp3vhl0zj7ddbzks9fy7ankp1n3i")))) + (base32 "04w6jhpc1vkqrm3dr5igp1iwkammmi53mqafjz694n379hamxrhg")))) (properties `((upstream-name . "powerTCR"))) (build-system r-build-system) (propagated-inputs @@ -10020,16 +10279,48 @@ data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (license license:gpl2+))) +(define-public r-psmatch + (package + (name "r-psmatch") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "PSMatch" version)) + (sha256 + (base32 "13w145is3d95392qqdq6qh3mrlcixbj0jzz4r590xas1qjp5d03h")))) + (properties `((upstream-name . "PSMatch"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-biocparallel + r-igraph + r-matrix + r-mscoreutils + r-protgenerics + r-qfeatures + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RforMassSpectrometry/PSM") + (synopsis "Handling and managing peptide spectrum matches") + (description + "The PSMatch package helps proteomics practitioners to load, handle and +manage peptide spectrum matches. It provides functions to model +peptide-protein relations as adjacency matrices and connected components, +visualise these as graphs and make informed decision about shared peptide +filtering. The package also provides functions to calculate and visualise MS2 +fragment ions.") + (license license:artistic2.0))) + (define-public r-protgear (package (name "r-protgear") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "protGear" version)) (sha256 - (base32 "0r8md32vxjzarjldr9vsh3k0ms4zgqm9c7pp2flanbyinnqlfnxv")))) + (base32 "1wbdp7f55lbn0gcxgnp9xk0y5npn7jmk9vp7yq9v76j7f396vj2f")))) (properties `((upstream-name . "protGear"))) (build-system r-build-system) (arguments @@ -10085,14 +10376,14 @@ batch correction and normalization.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "1gjva76nxa9nzzmc9hya3bq7hswfmjd768v21f6m3gyygxvl581m")))) + "0h0i4dgsgvyhma5pfvycv6wyxv27vp0b2i8b6l8hj55z8cvmvfln")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -10102,17 +10393,41 @@ batch correction and normalization.") proteomics packages.") (license license:artistic2.0))) +(define-public r-pwalign + (package + (name "r-pwalign") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pwalign" version)) + (sha256 + (base32 "1m0j1m5jif5spd9fkpzz3z3c9s8vwiy8xvpx8rz8igxj89rwrwb7")))) + (properties `((upstream-name . "pwalign"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics r-biostrings r-iranges r-s4vectors + r-xvector)) + (home-page "https://bioconductor.org/packages/pwalign") + (synopsis "Perform pairwise sequence alignments") + (description + "The two main functions in the package are @code{pairwiseAlignment} and +@code{stringDist}. The former solves (Needleman-Wunsch) global alignment, +(Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. +The latter computes the Levenshtein edit distance or pairwise alignment score +matrix for a set of strings.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0hxhl1l6qdi355w5y7fdq8vlba2pknfizggkgr2fp8f1f3zqh494")))) + "1n6rfrcvlgi6mzz36v9sniqr05xfjzvfdpv4xwsn1xq41326wdv3")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -10128,13 +10443,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.28.3") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "1d9icr17xwdmgm6b8ihrwxsg1fp342c2p9f8yqdjm2y52z88gmpd")))) + "0ll0sj2zyazw0nxbpybq9frmxvmcjkgk3hwp3flnysjxg056dhxg")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -10163,7 +10478,8 @@ the graph algorithms contained in the Boost library.") r-rsqlite r-rtracklayer r-s4vectors - r-seqlogo)) + r-seqlogo + r-txdbmaker)) (native-inputs (list r-knitr)) (synopsis "RNA-centric annotation system") @@ -10177,13 +10493,13 @@ library implementing most of the pipeline's features.") (define-public r-rcy3 (package (name "r-rcy3") - (version "2.22.1") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCy3" version)) (sha256 - (base32 "0qkjprf2p641j3a60av1l87pd6p17za5w6bp9qyah97jmm19za7m")))) + (base32 "03zmskcb8n87x6m5jlhsh2b0b2qjk91y16fdcj3kz5c1j7zfs18i")))) (properties `((upstream-name . "RCy3"))) (build-system r-build-system) (propagated-inputs (list r-base64enc @@ -10214,14 +10530,14 @@ with a single RCy3 function.") (define-public r-regioner (package (name "r-regioner") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "1qcgbj7d2fngs3p9a9apnj14x35kc651fy3m0651dnqrxz8j5yij")))) + "1ygdlqvhf165mqd247783pi1yzidqap8b913444vrs881n62xvrb")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -10245,14 +10561,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.42.3") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "109vmrdsjdjnfrlcdyadzbwz9a50hqaahf7dawwxkbbh4mmdih78")) + "0vq46dj2v3imjmf6cw8mab6k9v4rrc5r2vh100jjlsm3z15gvl17")) (snippet '(delete-file "inst/extdata/jslib/jquery-1.8.0.min.js")))) (properties @@ -10321,16 +10637,16 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.46.1") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "0yfy0y9ywzbbdmvvraxmizv3w2x1iznhfys6hhwyi644pxh4k3xn")))) + "086bnwzmlwq3z9a4kb1rnzb2wnchhi4gvzpijhladgd83nqyb0wn")))) (build-system r-build-system) (propagated-inputs - (list r-rhdf5filters r-rhdf5lib r-s4vectors)) + (list r-rhdf5filters r-rhdf5lib)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") @@ -10348,14 +10664,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "0cqf7k19k4m4swd2c1wd9cyzw9k90s3d3jq0hijjwvza50nn2dk6")))) + "0fsfp34pfb5k030j7nfx9b9vsil02y85sv1dd1y0bfdxchi4bw8x")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (arguments @@ -10378,13 +10694,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0bcapiwdzv7rqgs4hmw7hq290r3pz5vvhg4apxard0yybq83na1g")))) + "04lz0dzwmgi8j9wyspbmjln6yb5fv4f538nqyrfd31d0g16937b8")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -10445,13 +10761,13 @@ tab-delimited (tabix) files.") (define-public r-rtcga (package (name "r-rtcga") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGA" version)) (sha256 (base32 - "1lzdwkisvzj1wyx3wx4ll1c2j9ww3xz8kpbngmpf8cdrw4h3jrg1")))) + "1a967id4anjzpdlbdd8a85fvb1z7mcr759pr91aashv12bzzhnk0")))) (properties `((upstream-name . "RTCGA"))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -10490,13 +10806,13 @@ transforms TCGA data to tidy form which is convenient to use.") (define-public r-rtcgatoolbox (package (name "r-rtcgatoolbox") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGAToolbox" version)) (sha256 (base32 - "1a38b30nsg2bnlnijf4aa4rn4db2y4v86awfbf6a6qzqwlzknrcq")))) + "0l4idk6gsrnm7laj1xkm6jwmyy5l90kphm21zk7y33cpnp2ryjwr")))) (properties `((upstream-name . "RTCGAToolbox"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -10529,13 +10845,13 @@ pre-processed data.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1jxhv2fq62lz0j6kbwq43c8ggk14ccsjg0xgfqjqy941dj9ig0n2")))) + "0h2cqr1jqqqxvkmqpngfl8ppm1p65vvlb1wgfwl9r4f99b8vz33g")))) (build-system r-build-system) (arguments `(#:phases @@ -10549,16 +10865,17 @@ pre-processed data.") (native-inputs (list pkg-config)) (inputs - (list openssl zlib)) + (list curl openssl zlib)) (propagated-inputs (list r-biocgenerics r-biocio r-biostrings + r-curl r-genomeinfodb r-genomicalignments r-genomicranges + r-httr r-iranges - r-rcurl r-restfulr r-rsamtools r-s4vectors @@ -10608,13 +10925,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-saturn (package (name "r-saturn") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "satuRn" version)) (sha256 (base32 - "12bivj0cnp38apwi3jqmil8bwsfa96cjp5f132a5raacd2z87gqf")))) + "03mlb4j219w8760zm5hnryjwxns3qz9y3wl6zaqdfnl94bwyl9r8")))) (properties `((upstream-name . "satuRn"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -10642,13 +10959,13 @@ transcripts in groups of interest.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "13wrxxdwphngi0f9vxakykk54bqngw8g38w6wkk96999lzb3p57p")))) + (base32 "1gzssp7im1d9pp2mbar27k854fcc3rqyza5d77flmhshq88xrskv")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs @@ -10679,13 +10996,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "1f3n1m6fjx965wm2jllzk51ssj92ifxb4bln4vwk25qxd3g0bna8")))) + (base32 "1np3arhjxxgif68i0wi0nqqbrwavy14dh9vy2g9mw4408k7789w0")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -10725,13 +11042,13 @@ comprehensive scDblFinder method.") (define-public r-scgate (package (name "r-scgate") - (version "1.6.0") + (version "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "scGate" version)) (sha256 - (base32 "0h12d36zjc6fvxbhkxrzbpvw49z9fgyn1jc941q70ajw1yqi2hhh")))) + (base32 "0zlbrvr6lxcihspfqgpvv5kyrzqqpy3451j0kpnqc0n93bbs4cqk")))) (properties `((upstream-name . "scGate"))) (build-system r-build-system) (propagated-inputs @@ -10804,13 +11121,13 @@ method applicable to massive single-cell datasets (>10,000 cells).") (define-public r-scmap (package (name "r-scmap") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "1sd5ixs8fbiqqp1p4p505l1f0lncmagkhzh4xrk8wrca6db6k6d8")))) + (base32 "0acy3sg4j36znsfxpkb190wbawbngx15cr5x2lhgrjivvw3637x1")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -10846,33 +11163,41 @@ different experiment.") (define-public r-screpertoire (package (name "r-screpertoire") - (version "1.12.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scRepertoire" version)) (sha256 - (base32 "1wgs8dv5zl82iciy86w5ws1gq8v2piklcifbw7gmbw60kijyr2l1")))) + (base32 "1ifnyfzswisacvxxf041l1snfv1b8x30pjg2pwampg804c56f1wj")))) (properties `((upstream-name . "scRepertoire"))) (build-system r-build-system) (propagated-inputs - (list r-doparallel + (list r-cubature r-dplyr + r-evmix r-ggalluvial + r-ggdendro r-ggplot2 r-ggraph + r-hash r-igraph + r-inext r-plyr - r-powertcr + r-quantreg + r-rcpp r-reshape2 + r-rjson r-rlang + r-s4vectors r-seuratobject r-singlecellexperiment r-stringdist r-stringr r-summarizedexperiment r-tidygraph - r-vegan)) + r-truncdist + r-vgam)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/scRepertoire") (synopsis "Toolkit for single-cell immune receptor profiling") @@ -10889,25 +11214,35 @@ powerTCR R packages.") (define-public r-scrnaseq (package (name "r-scrnaseq") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scRNAseq" version 'experiment)) (sha256 - (base32 "0dbh3sqq7lkkdf7vls5qg7fbn6y74c7hsigb4d69pvk934ll88aw")))) + (base32 "0jsq037ba4xsb3bwwf021jw2hqv30vb5nrjag97xadx75z5fzqlr")))) (properties `((upstream-name . "scRNAseq"))) (build-system r-build-system) - (propagated-inputs (list r-annotationdbi + (propagated-inputs (list r-alabaster-base + r-alabaster-matrix + r-alabaster-sce + r-annotationdbi r-annotationhub r-biocgenerics + r-dbi + r-delayedarray r-ensembldb r-experimenthub r-genomicfeatures r-genomicranges + r-gypsum + r-jsonlite + r-matrix + r-rsqlite r-s4vectors r-singlecellexperiment + r-sparsearray r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/scRNAseq") @@ -10921,13 +11256,13 @@ with cell- and gene-level metadata.") (define-public r-scry (package (name "r-scry") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "0hbdsjsn0jl0dr2ly5vx0wb4bnz7nl15kkypryywjvis9rdasjj3")))) + "16489ff1nc798nfcmqvqaczm7hqffkhpad1dfgr7dxlahd8sbnw9")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs @@ -10952,13 +11287,13 @@ single-cell RNA-seq.") (define-public r-seqarray (package (name "r-seqarray") - (version "1.42.4") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SeqArray" version)) (sha256 (base32 - "0k7g4wkj1l35pjy6gb3bdlmz5g8q2d596glj09ggm73aaj3z4m9d")))) + "1g8867y66f8ihr0w2shc17wxnavnkwn9y25f850nwvnn9nsbk88k")))) (properties `((upstream-name . "SeqArray"))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -10982,14 +11317,14 @@ data access using the R programming language.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "106359wn4v0m53b33x4zjsyjsj4j8h7bnvd1whamsig982h6szp2")))) + "154c3g4i6snsi8vkwjw4d8lyr3372d6vyw237nslw1y5n837yzir")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs @@ -11005,13 +11340,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0rs9dy540d4agp7fc8glbrcnly4s6qcxqsq4yv8y555bbdld6dv0")))) + "0iv0dhs1z8i0jglh1iw6ypzh6qslnn5xly2kjfxaxk9cggnjb5h6")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -11028,13 +11363,13 @@ reference point and sorted by a user defined feature.") (define-public r-sesame (package (name "r-sesame") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sesame" version)) (sha256 (base32 - "0yh4mrsj3pqhjkrq5dwmcpcqwixs0pmjy7dfa3cr0mf52fgzcvmr")))) + "0qz4vhz1iczz4n4wigzqkmkbsvq5ql04x1gawxv4f8ii61npp0h4")))) (properties `((upstream-name . "sesame"))) (build-system r-build-system) (propagated-inputs (list r-biocfilecache @@ -11070,13 +11405,13 @@ and advanced quality control routines.") (define-public r-shinymethyl (package (name "r-shinymethyl") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "shinyMethyl" version)) (sha256 (base32 - "1gkj15q1rxvsdzbsp3gkk02kvvx0kq4wsqycf3ln1bszb9688jw6")))) + "15r9x1fqladjviyisbhr8zff0a6g9kvbvx72xcp3bfadp3wpygds")))) (properties `((upstream-name . "shinyMethyl"))) (build-system r-build-system) (propagated-inputs @@ -11098,14 +11433,14 @@ methylation array data. Both the 450k and EPIC array are supported.") (define-public r-shortread (package (name "r-shortread") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0fgiszb5qhplppfngpi4s33sx62ff5sdhd6n31a3b6l7fnlvk51m")))) + "0x5iqx2k2xs5rwjch0bpcb8pgc0nhb571991yahdr8hsxwbas3jm")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -11122,6 +11457,7 @@ methylation array data. Both the 450k and EPIC array are supported.") r-iranges r-lattice r-latticeextra + r-pwalign r-rhtslib r-rsamtools r-s4vectors @@ -11141,13 +11477,13 @@ ungapped alignment formats.") (define-public r-sictools (package (name "r-sictools") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SICtools" version)) (sha256 - (base32 "0bcajjvkaxmr8bdij8xln7a3nmxbm7jkjvg2v6p8kd0xr3q9a70q")))) + (base32 "0ymk18aj4r0526xqqkrvd75p4jrgrq2wshx7mqh2wj7nizjfn8fv")))) (properties `((upstream-name . "SICtools"))) (build-system r-build-system) (arguments @@ -11184,14 +11520,14 @@ less than 2bp on both sides of indel region.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0qhrlhf881mi2v0n0y410c0bf2cm3imrlglq8argnw86n9xj51pw")))) + "1031rkl2gcgx4k1biz4bc38hfq7r6diqk48769jhii0r06ablrhi")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -11225,13 +11561,13 @@ and comparing the clusterings.") (define-public r-singscore (package (name "r-singscore") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "singscore" version)) (sha256 (base32 - "0hafzbhbik1512pisjvnnzmy8pl2shrgra6l06kpvsrczkqlmi04")))) + "12avzrc16mxz7v8jp4rxz5ia6008rjcja1h3hd0n60z644w9cng2")))) (properties `((upstream-name . "singscore"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11263,13 +11599,13 @@ level.") (define-public r-tcgautils (package (name "r-tcgautils") - (version "1.22.2") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAutils" version)) (sha256 (base32 - "16pcz52ynx0syb5bcnkywllqxcfp7jipqgzgjr7q70k1z13ah7a3")))) + "0fmz1lfpn8ws584q4xlicg897qs36wgr78crw0d9415ci6qqb4r8")))) (properties `((upstream-name . "TCGAutils"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -11302,13 +11638,13 @@ identifier translation via the GDC API.") (define-public r-tkwidgets (package (name "r-tkwidgets") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tkWidgets" version)) (sha256 (base32 - "11a8rflmga2d63l5nzdlbkyfnzsf20dzg2sy6qr143hg9sjzqrrj")))) + "0k1d5r306mbry0h7yqp246i13adxlmxl2vhwdsfgh29v8qkg1szl")))) (properties `((upstream-name . "tkWidgets"))) (build-system r-build-system) (propagated-inputs (list r-dyndoc r-widgettools)) @@ -11321,13 +11657,13 @@ identifier translation via the GDC API.") (define-public r-toast (package (name "r-toast") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TOAST" version)) (sha256 - (base32 "00wpgs2zdrgrh9xmp6m5h9xgv85mhdi36qvwg9gwbz9i7cfabmy1")))) + (base32 "0srjx9z59a65nhrxbzxzxnkyn28zskc6z4p8drihq1lhw6mvdp4r")))) (properties `((upstream-name . "TOAST"))) (build-system r-build-system) (propagated-inputs (list r-corpcor @@ -11356,17 +11692,16 @@ tissues. Current functionalities include @end enumerate") (license license:gpl2))) -;; TODO: check javascript (define-public r-trackviewer (package (name "r-trackviewer") - (version "1.38.2") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "trackViewer" version)) (sha256 (base32 - "1zgxp76ykgn4wk6nnpafjpswcky23jpghzzs68z0hhlzv4cc40s6")) + "01m0jwig3l6dfhd3w5aq4sx2krsipjg5jjxa78kalfrzrm6k05s4")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "trackViewer"))) @@ -11390,20 +11725,20 @@ tissues. Current functionalities include r-genomicalignments r-genomicfeatures r-genomicranges - r-graph r-grimport r-gviz r-htmlwidgets + r-igraph r-interactionset r-iranges r-plotrix - r-rgraphviz r-rhdf5 r-rsamtools r-rtracklayer r-s4vectors r-scales - r-strawr)) + r-strawr + r-txdbmaker)) (native-inputs (list esbuild r-knitr @@ -11426,13 +11761,13 @@ methylation data.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1lbla2syljpmgdf7da7vl1260fy54xs3hk6m2gjpark0dka0kqbh")))) + (base32 "1lx11dyr8q4yd57l7rj0788488amhiiahfml2m69554hk94cd46i")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs @@ -11476,14 +11811,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "178v5r0nck9ils5k7hj92x7z1xk5zq6zyc78wqnz7s3shbnq9ld7")))) + "15q1mq48nclf2lqc2v769q79frrbm2l65d54vcqg06b861q2wq9h")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -11503,14 +11838,14 @@ structures to hold pseudotime inference results.") (define-public r-trna (package (name "r-trna") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tRNA" version)) (sha256 (base32 - "0mcpql3zf1gw2k6gfyqycycc8li00818gd9qzs8s3wva7kxbpn89")))) + "0dg4s5kxsdh2j8smqi8vm7yncy9kb79sj8xlvf4wgf3aljarms21")))) (properties `((upstream-name . "tRNA"))) (build-system r-build-system) @@ -11540,13 +11875,13 @@ additional column data sets.") (define-public r-trnadbimport (package (name "r-trnadbimport") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tRNAdbImport" version)) (sha256 - (base32 "1i2mismx914ijys13wwz50gkk682rklp36aci270nc7vx78hynni")))) + (base32 "0yvgxxf5d5mh91cmbba66krj6jz5gl1qkgjck9310k4mk7pjfww3")))) (properties `((upstream-name . "tRNAdbImport"))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -11570,13 +11905,13 @@ additional column data sets.") (define-public r-scds (package (name "r-scds") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scds" version)) (sha256 (base32 - "0cmzvc1m29ijhzs2p407bhhxfqbflzsnrk7nq0jshjyw6v6pkfn0")))) + "19xma4kmx8s6m6dvqyw461ahqyfqb7z3n5dz4ppab4xcpmqvx0vh")))) (properties `((upstream-name . "scds"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -11598,13 +11933,13 @@ scRNA-seq data computationally.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "0q3j0jpc4mnmjb3xha5cmfhk1qdr1jiz7kdghznk4zqxn4bchc1d")))) + "055dylajbn94khi0829qhxx0lbn1pvh30xw09gjn1jvxsgzj49nc")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -11670,13 +12005,13 @@ tools either included in speaq or available elsewhere on CRAN.") (define-public r-spectra (package (name "r-spectra") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Spectra" version)) (sha256 (base32 - "07zs9x5fzxzwicjc5x29sv33yidmq1ar70ss91py094zbw9i63qy")))) + "1ibbc3gkzh49cj45j2qdhsjhyrjj4ly3wckksiagc73wfag5hd2s")))) (properties `((upstream-name . "Spectra"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -11702,13 +12037,13 @@ data sets ensuring a small memory footprint.") (define-public r-stager (package (name "r-stager") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "064hvx8qyw5hdhihwl9k0jqhg6saz4ng2m37d2ipr5pz9v8adspb")))) + (base32 "0ayjwv2i9q8dzq5pzhyzkxzkz9ycka2v6ccvq5y9cg7x0mw4qvbh")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -11725,13 +12060,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.14.3") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "06bckzczg2rspazcbpp3v265c1dkr9l1vpdhkc7gdn2dk960jlkh")))) + (base32 "1bn21hqvcl1a4knj7iygwqx79s49ggjaw30fj6478h7khha6556b")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -11758,13 +12093,13 @@ that integrates the various evidences.") (define-public r-structstrings (package (name "r-structstrings") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Structstrings" version)) (sha256 - (base32 "10j1khhjd30wn9yfz4jhgx34z0yyijgwgydr8ric52337vwpx6dl")))) + (base32 "1ka9kixhgc9vfar18fzd8vd5ydmdkqa2s6xsmhlh927zrijs3vz9")))) (properties `((upstream-name . "Structstrings"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -11792,13 +12127,13 @@ large extend by the @code{ViennaRNA} package.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "1h3l3xbxwf2w2dl0qz72v68h5g77zhd2rr0g86l2dhn67mhy8ml2")))) + (base32 "0hnpa6ykfasp2hshqdny29dyw6y9dib4rsm379fm7n8iami1rjp1")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -11809,6 +12144,7 @@ large extend by the @code{ViennaRNA} package.") r-genomicfeatures r-genomicranges r-iranges + r-pwalign r-rlang r-rtracklayer r-s4vectors @@ -11829,13 +12165,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1949k2658drmcrrr7v6748b40g2qym39n0ch50jxf0xmmlb1r04z")))) + "02cvgq2vgg0gz1gxkc4vnr9jg4wkj32bl5a1qyv77wnw2b2v5hp0")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -11864,13 +12200,13 @@ samples.") (define-public r-survcomp (package (name "r-survcomp") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "survcomp" version)) (sha256 (base32 - "18a81vv88xj3frkdy5l6w2fc4xzr1k6vgbz4j4marlmh6mz6skin")))) + "090dl580cwicn3px1khkhcix25snig0k7phb7z3nzmrbxmp82ygc")))) (properties `((upstream-name . "survcomp"))) (build-system r-build-system) (propagated-inputs (list r-bootstrap @@ -11891,14 +12227,14 @@ of risk prediction (survival) models.") (define-public r-sva (package (name "r-sva") - (version "3.50.0") + (version "3.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0p4zgw1pi5vnaqxn6jmvhpy0h5hnnqp41n0k2v0chhqgqxgn67x1")))) + "07iq894mf5d66cxjl283pcvj1frj56pb15z984d4svk6f5cacg3z")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -11922,14 +12258,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "01amqib9ahrf19xpy4ivlsss82zyp3w7fbgwrwp53zfbg0cninga")))) + "13xxcqy5hhy45zglv6gc86ndmisfkjq4dg55x2j1kw3jqha1brnx")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -11965,13 +12301,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1sznyx11kzw8d8zg5ynl9sp6m0daf2yw3f2b24maxbpr1xkif9nx")))) + "0ly4rai3na88dnfizsi60r6py0qmf0pw95b0hprfkvzpjyd72p75")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -11995,16 +12331,57 @@ dependencies between GO terms can be implemented and applied.") ;; Any version of the LGPL applies. (license license:lgpl2.1+))) +(define-public r-txdbmaker + (package + (name "r-txdbmaker") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "txdbmaker" version)) + (sha256 + (base32 "099x6v4crp953jcgqipj0001kxg7gv5h0r4mmvh1cg7j69w0zd5m")))) + (properties `((upstream-name . "txdbmaker"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocio + r-biomart + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-httr + r-iranges + r-rjson + r-rsqlite + r-rtracklayer + r-s4vectors + r-ucsc-utils)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/txdbmaker") + (synopsis "Tools for making TxDb objects from genomic annotations") + (description + "This package provides a set of tools for making @code{TxDb} objects from +genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). +These tools allow the user to download the genomic locations of transcripts, +exons, and CDS, for a given assembly, and to import them in a @code{TxDb} +object. @code{TxDb} objects are implemented in the @code{GenomicFeatures} +package, together with flexible methods for extracting the desired features in +convenient formats.") + (license license:artistic2.0))) + (define-public r-tximport (package (name "r-tximport") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0m6avd815xcv3py5sym083pdccvd4crdyyc7sfpxccnksgchyrf2")))) + "0wayib05k976wivf9xgbfz5mfvi5hmxj3wm6zw031bj4w8dkc1v6")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12023,14 +12400,14 @@ of gene-level counts.") (define-public r-valr (package (name "r-valr") - (version "0.8.0") + (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "0jf47yfi8dr8mgqv1gbl2kd7wgyiwsnipiwfdhf9l346yg9aj96l")))) + "1pp8naglh26yi8c2p15arx8jkj3jyslzw7j3n5bnzngdpfprk3as")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -12057,13 +12434,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.48.1") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0l9xkrvsrc3m65kdjcyir6jkpa718g7idziwr0pp5yaj84bd3xia")))) + "0slvlhm65hkjspzlzs3gi04a6mlfwvda314z1nmzpdi3y5111fg7")))) (properties `((upstream-name . "VariantAnnotation"))) (build-system r-build-system) @@ -12096,14 +12473,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.70.0") + (version "3.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0li0yxf8m34xpmrgv5vciy8zdsbfdlajl9cmnxr4g4nmarik2bkh")))) + "1r6cd92d4xlx4zdyy1sfaxicjf4q3arflmswpdkckkc4h9c6zf8m")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) @@ -12165,13 +12542,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "1cnw2zbjfs8qcgqrx557g00m59h5pldcx788v9r4gn2f70rx7vx3")))) + (base32 "177yzqmkf3f2xgfrz1zpcw554yzm4njd2chhmvxi2vvijvnrgdf3")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs @@ -12201,13 +12578,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "0pby2h8m12xlngpk33dvh3nkrpgqi4f2mb7g9jafyiv3sl8pjd19")))) + (base32 "0laahd3v5m313q1iq259aikgqf7zlmpxyxhws2pr7vg97g37bbhs")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") @@ -12228,13 +12605,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.42.0") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "0h03imdl0pyy714kmddsdnsv69bd8kr7bhi9wq9z18y8ahg5cqx1")))) + "0fxv97m79w0ph4wbgp9drz6ahvnnzpv08grb11lr6a7laqq5x8s2")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -12262,13 +12639,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.48.2") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "078v1iywzc0ng27r0wjchvkh4znzydq1swlalqb95xkmn72vrq8d")))) + "155q6983xjdjpq445lpg5n9gzf8gr18nll6dmjk7jwdq7fdxb602")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -12282,13 +12659,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "029bqn25c90algvgacxbv0fdznpg879xjwfj5hiydfwq30y0kr8r")))) + (base32 "13qkj9adv5is4fas667kxzc2zgni3ayl5hbimakq8y4mw6qj04dn")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -12314,14 +12691,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "0zvb84jlsvmr2dvwyy4xjqv353qrxpls0v2vz0nmj1q4m7lrpl1k")))) + "19znr3vwp20x84jiwy0im7s6vd8a71yng8w2ji88ffzq0xdkyyjm")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -12341,14 +12718,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1gdvjvyjfpvvrqyj9rq1l4dnq00hr8vr8knnlb9gnjk21sbcf1d7")))) + "15icfcmpwrnjpyahc4v168fpcbsml6x7h4drmsyh9l8d1284yb4n")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -12376,14 +12753,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0pqn5qslynylx235wknwj71a6j7xf5i6pb7wjm00jwrdbqwvdlp6")))) + "0mv031fsy1g3k0brxx8z7d1ryg0z2nxihrs22n6ln2jk240lkyfx")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -12412,13 +12789,13 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qfeatures (package (name "r-qfeatures") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QFeatures" version)) (sha256 (base32 - "1g744fpb6g690bjbjs4v2899wwv6qc7n5cyq977pm8f3wln0m7mx")))) + "0qkbbpgkrlk8k4mj3463pdcimdvpx201gk55wil6v6z56yaifsc5")))) (properties `((upstream-name . "QFeatures"))) (build-system r-build-system) (propagated-inputs (list r-annotationfilter @@ -12432,7 +12809,9 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") r-plotly r-protgenerics r-s4vectors - r-summarizedexperiment)) + r-summarizedexperiment + r-tidyr + r-tidyselect)) (native-inputs (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/QFeatures") (synopsis "Quantitative features for mass spectrometry data") @@ -12447,13 +12826,13 @@ proteins) in a coherent and tractable format.") (define-public r-quantsmooth (package (name "r-quantsmooth") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantsmooth" version)) (sha256 - (base32 "050nnwhxk3ld615f6ij4cc3d6wzrrxykvv02fr20fg5gzdj0z08a")))) + (base32 "1mgdrhq0j4b29l3y49h00ccwkz6vhs6hjb1236blmlzdf590q7gc")))) (properties `((upstream-name . "quantsmooth"))) (build-system r-build-system) (propagated-inputs (list r-quantreg)) @@ -12474,14 +12853,14 @@ on the location of the probe, and other useful tools.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "10v5khnrs1fa84d430zy52f9466rwb1byaw1l3c9nivbhmaxhvyi")))) + "1hgkrvbs1rf8db105ik9ar54zdx49v25hn71jgw7j5r43zngfg2a")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -12529,13 +12908,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apcomplex (package (name "r-apcomplex") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apComplex" version)) (sha256 - (base32 "1y3c3358y7ynn5lj2gcy9ll2gxnnlv689pj0bgr2gsnhbss1kw1r")))) + (base32 "1fsqrds5r8bhdf7fbnw6rf3vqapl6xk1a5l6jjb98raxmjsrfyqs")))) (properties `((upstream-name . "apComplex"))) (build-system r-build-system) (propagated-inputs @@ -12554,13 +12933,13 @@ spectrometry} data.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "0cj9yzmh9w3fk3rxmk2k5j55r42mmz9znszmr4l160mr23alkzx4")))) + "0l84sf4ikx0q031wf0k26n9ikwmgs4nm7v7bky47q3ik29mh7wgs")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -12581,13 +12960,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1k974cvfbkl8ffn7k2la843bv2pf33cr5f6fahiiy24d68lxwifr")))) + "0dj3pcycnjll8z1r61l6gnjvq74w2l0glrx6hqwcqvk5j7ixcdz7")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -12608,14 +12987,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1nlcx4fl1cpcg38cn9p55f75bv6pcg6h2jv4z94g2b7g1gwjd686")))) + "1sr0zy5pbjmjzkwkpjmr26k4dcf3f3kxsl7z2nqw0p0a14rh57pm")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -12686,13 +13065,13 @@ processing to visualization and annotation.") (define-public r-mbecs (package (name "r-mbecs") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MBECS" version)) (sha256 - (base32 "1j7vb26n2fnf5fkk8hfz552yx91g4zg719alhg4hg2vvjd1qx2l1")))) + (base32 "15nv5rbw158d071gscms6p42wzf6ibnabiqcq256rcz6j0r69b63")))) (properties `((upstream-name . "MBECS"))) (build-system r-build-system) (arguments @@ -12736,13 +13115,13 @@ before and after correcting for batch effects.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1x7azijfs28iz2w40b9hnpgwh4jxgihl8cj6h91b2wgz79sq649l")))) + "0fnf6ymbcfchhlcbwpwlcq1jc3lfzh9f8mf76xfy7vrpwngds1fs")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12768,13 +13147,13 @@ large datasets, including support for on-disk data representation.") (define-public r-multibac (package (name "r-multibac") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiBaC" version)) (sha256 - (base32 "1mwfibakrxgs3r572bqqqmzq7ys6cs0bpn0wfrcb08ww2197xc4j")))) + (base32 "0m08620sii9181y0vlcrw9nbcnp4vnjjxvp96iqlgg5fsb23wbl7")))) (properties `((upstream-name . "MultiBaC"))) (build-system r-build-system) (propagated-inputs @@ -12798,14 +13177,14 @@ the batches considered.") (define-public r-multtest (package (name "r-multtest") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0s8x2rg2xp6awg2cikybgxrxpi9f91jah7dskk5dnfkazd20di4j")))) + "04dv5rcqwpv0im7j3hvcj8hjybgs4a384zgnjyqbcipcicd2rjz4")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-mass r-survival)) @@ -12833,13 +13212,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0p7g7ykpkngbs3h1dsackfy93l8lvc301lr64ffsiaw60gllcx01")))) + "1wa10s9a8p6lajim1lbw4rxyc4fz7y6fpymrh0c0ip85971cd9hv")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) @@ -12876,13 +13255,13 @@ fitting of some classes of graphical Markov models.") (define-public r-ggtreeextra (package (name "r-ggtreeextra") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtreeExtra" version)) (sha256 (base32 - "0q8k81mq5q9fym4zyrkzapgyww23lkxpkyj2s9r1y0ciclk90zdc")))) + "1wy229rnp356hi144flm9fvhv414jxmxc967f7pyqwl4abiwlmzm")))) (properties `((upstream-name . "ggtreeExtra"))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -12976,13 +13355,13 @@ a given recall, F-score for single and multiple classes are available.") (define-public r-pepsnmr (package (name "r-pepsnmr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PepsNMR" version)) (sha256 (base32 - "013jw9l7r87j4bmpjrvq5qn91kp44wj5vd68cl5axbqhjg7fq4ww")))) + "0z3kw8j972zmrcyikag5js20zpgc3l5bgkn5q31dzi1q7ynpkwhv")))) (properties `((upstream-name . "PepsNMR"))) (build-system r-build-system) (propagated-inputs @@ -13033,14 +13412,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.36.1") + (version "3.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1jmg958v8ai9v3mpizj24nc0vsl564inndm0irflprs1ky90k8vl")))) + "1g7p53g91xx3x10kad2f190bmg10ryp928m0q5wxz9n8lycb5rgl")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -13048,6 +13427,7 @@ determining dependencies between variables, code improvement suggestions.") r-biocgenerics r-biomart r-biostrings + r-data-table r-dbi r-dplyr r-ensembldb @@ -13062,12 +13442,18 @@ determining dependencies between variables, code improvement suggestions.") r-keggrest r-matrixstats r-multtest + r-pwalign r-rbgl r-regioner r-rsamtools r-rtracklayer r-s4vectors + r-scales + r-stringr r-summarizedexperiment + r-tibble + r-tidyr + r-universalmotif r-venndiagram)) (native-inputs (list r-knitr)) @@ -13087,13 +13473,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "14x5jib5xh2006lg96v3b9n2pnbjcbsd5igqybqsv0c53rk9394d")))) + "1r7n5p89460h47mnfh190184dbcmrbj0j5d7dswkfwh6ixan3zyc")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -13114,12 +13500,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1gj4mdbni5fk2z3zrk2cnhy610ihhhwjb9l1crglkklwxhkqlkvd")))) + (base32 "1h96aq92bad69ycrmrvxwdz8dg9rk44925gj83gxzqypw88j2x0y")))) (build-system r-build-system) (propagated-inputs (list r-limma)) @@ -13133,12 +13519,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1iw03gq1kvmn9a6h0kw389l9i7h99fbxcsag9f3gkfznjv0vp5k4")))) + (base32 "1fz39fdkfvfhzm69pfvliqvp48wsldwm3kpgbsaacrdh46jg5vzk")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -13152,12 +13538,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1x2zfr40bm42zd1bljwpbz3cz1q23a3yy1g277lwsp78gxbn3zly")))) + (base32 "1gjd3ggiw93cwcacjb1472ia98aaapj9gln04v5pbwmp2r4xfcs7")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -13171,12 +13557,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1n2qngqqw3hfv1yscksnpg8wslc85dlvaqw1hz2qvsxf1gcq2mks")))) + (base32 "1myk6qgl45ya7qw6sx6xc98d8m5ffl2ghm3zvqmyh9r0sp6x184f")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -13203,14 +13589,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1b5vvzl0kkm6kb03vr6m6sdlr3azpc24933a7ayxkiffmf2wbi0g")))) + "0nlkynzijxl6f8983vdpmcssvrpjf6s42zx3lxfwxwlhrvz1yg9l")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -13227,14 +13613,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "061d2z1rrcyad6cf19si14ab9a3dxdi17sfbkx3vx8kdsfs3djy9")))) + "013lmgdkj596gqzm0nlxjqpv0w94hap9vndp5znqpk4inq88gj8m")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -13261,14 +13647,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1bd37ypxsj9p94p2851hhc9ind59b5pkg1lyalha1nfw5gf8iay3")))) + "0h0sxmg4knsarh7w7dnp539cs9sfxjw4413q1yyyz3gbi23bzww4")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -13302,14 +13688,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1cigbp3pc70ipja9mmprkrs91723r1zwgxbzyp87n5mb0i4q8xqh")))) + "0p0q28n8hlai80pxxns9pzzg552pbwlxlph8zjf78bwbjagrfbz5")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -13319,6 +13705,7 @@ assessment, principal component analysis on codon coverage.") r-genomicranges r-iranges r-rsamtools + r-s4vectors r-seqlogo)) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") @@ -13330,14 +13717,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0mpgxcwhb734pyn6bj93xknb704yrjkprxpa7kqwl24rbqyjydqs")))) + "0ikkmhz6grmhksmyypj9hqmblls4cgww0dx4kzg4cy5bpavsq1hs")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -13364,14 +13751,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "13rnxig22agykzv3q7wm4wr9c5aw56q6q1zv8m5g5ngjcssy8l4c")))) + "16aaaa4nr1y5ng1hzw87q950clid28iqf4gkypcpihg3cz69axxg")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -13405,14 +13792,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "10a83rr0qhnzdhvlbyn0y690hxnl8q86z47dpimr6sq41w463im3")))) + "09whaam2r30dq8y9r6vvc0r4sisz78c921bgx7wj6cmn2nvpgf9q")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") @@ -13451,14 +13838,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0pkh15jjjb83pq7d49yzwb2gyc95x4rww78qnzpdrzhycgmcapii")) + "1d7rq3irp3n0fabfgjs2x2c9lscz70a38qf3wbxvi417qn7fpyla")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib/" @@ -13536,13 +13923,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "0lbsavr9mhka8s7i056h4jjb1v36v3sshrhdz74n8qadm7fy59l5")))) + "1my8v0zx5xsxjf8dj2yw92b8zp725hxhb2vrl5ccgz2w9xkn0dkj")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -13572,14 +13959,14 @@ experiments.") (define-public r-rots (package (name "r-rots") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "1zd5w3mq0vjs3ivdb23x6d28sqq0dsfv13d64k1yijr4vdk3wvp6")))) + "1s9hr64gpz08j638wlglcmk6c8yyj1hzrgddiphklkapc1asr320")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -13595,14 +13982,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0s5hia3xvddi0gaawcr5zsh34v6sh2zdi5gsjis8ar2g2p7agqgg")))) + "0my4jpxw3xy9n40cqvdaz6ay7gpwshn2iqxr43knrk0ckpyxx2cr")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) @@ -13619,13 +14006,13 @@ genes or proteins in these datasets.") (define-public r-plyranges (package (name "r-plyranges") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plyranges" version)) (sha256 (base32 - "1z4pc9slbd6ji3c6g9flxhvvf0anjmywrlnjblv1mpgsh88avp7w")))) + "0rh5l6bd80nhffqpnnc2c00mvp8p32ykld05h94c3y8c9mvmsl58")))) (properties `((upstream-name . "plyranges"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -13653,14 +14040,14 @@ accessiblity for new Bioconductor users is hopefully increased.") (define-public r-inspect (package (name "r-inspect") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "04znack6p50cmc2qyk4hf45m6v70p0bv7h3xs87j0x0h4mb920ch")))) + "0147ss218d3dnqbdgfwsg24an63qln8l5kkv0y4hm56bncdrm1i0")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -13699,14 +14086,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "12x4k55kshvwyzl83zkgkp0ylryr8wd3kz44ngp60k4pkwhkl9h9")))) + "0vxxg6fkgck640p9plk4vx3d05794s3xgxksv819d2wicvyby4hk")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -13726,14 +14113,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "04byggwsvmqrl77268smbas0wax460cdshmp4v5iqc5fghl7n0p2")))) + "0i91kjwransy6l217rmxfzfchb43h1sjk8ygf0y8a3rv6rp7ylfd")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -13751,14 +14138,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0lvsw920i75di5pwq7yvk8wcxp01wrh7863xmwbrmk5jrvl3y4h4")))) + "1krg4cs406ymk27qcj3j1jsl8vl4j9k5zvwf4vzxgbw3x6lpywid")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -13779,14 +14166,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "1aigca0s8cmi46458pl9p9vwlkrmqawbgi0xmbwslz646x2s2h4a")))) + "0c6sp5nps31ygrr7lxxc2gbg19qsk107v23x8f6acqk1xwlsfppi")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -13805,14 +14192,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1kvzdryw74r74gwxddsrng81ww49p3s7hgxn8ggl0p8fvz3sfgir")))) + "0xfjq13yirfz7dzzlf2m60lk8xb3qh6k5hr66ygvjnm716x3vyh1")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -13822,7 +14209,8 @@ multiplication.") r-magrittr r-rlang r-tibble - r-tidytree)) + r-tidytree + r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/YuLab-SMU/treeio") (synopsis "Base classes and functions for Phylogenetic tree input and output") @@ -13837,13 +14225,13 @@ platform for merging tree with associated data and converting file formats.") (define-public r-treesummarizedexperiment (package (name "r-treesummarizedexperiment") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TreeSummarizedExperiment" version)) (sha256 (base32 - "1yvqixlivapasx0ircfhmc8ckr7sw86d9vfvnqj97p4r667x6z6g")))) + "0ygzw9nba5pxgrbib8sm7qwhzzm8m038banb0z7n42vkb1cb3d5i")))) (properties `((upstream-name . "TreeSummarizedExperiment"))) (build-system r-build-system) (propagated-inputs @@ -13870,14 +14258,14 @@ data.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.10.1") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "1p475vh567q4szb8hy2qk72pvqh5rlbyqfjcdd0i83fa2y4bi31d")))) + "1bm7c46k8qbajjvl8475b7fcd0dvg9s1bir8313qgm466qm6immh")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -13908,14 +14296,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "05cy3xvj78n2p9l2pxfys7aczr51gm2ywprn4qmzr7ppb6rq5f66")))) + "100wsg2y7069r7xk5bsk5n4n8dqvpbk297w5ishnijrvxhbs9f8n")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -13937,14 +14325,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "0z1p02329wk2x058ij42q5pyvp0vhsihaxmizgzcj4sww6i28j33")))) + "1xl9wn3slj3ywjglb8zq2p0ifx4xwxbqsm99fjlf6hanfhmnxyay")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -13972,14 +14360,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "06xwyqlsas98lxmd0qw5ysjwbk397kyapd5jq5pzjrynsj4r9xn6")))) + "0w7j6xh0gzhahk1r8w2wgnylq5v476jzz0g14yjmszfkzm10va3h")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -13995,6 +14383,7 @@ possible, parallelization is achieved using the BiocParallel framework.") r-rcpp r-rcppeigen r-rcpphnsw + r-rlang r-rspectra r-scales r-scatterplot3d @@ -14037,14 +14426,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "04dhkm8cq87x3c9f114z6q1pcw77xgs33rmhgzk4ajzxywhklq4j")))) + "0y39fpbnykqf5ycpi9q3rw73dkn2ksll7n6nafimxvxsh463d8ky")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -14097,14 +14486,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0hyjin75v8l2a8qymsd6rjb8m7svv2q07s6z1dllqag09wja1yfz")))) + "1q4s6rb6iv9cmfkjymgdyb4h3z0x0kzzd2bvfdjrzzzza6vhjpxl")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -14195,14 +14584,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "07x9fh8akgiixsv1xddkvs2q8xxfsibas01kdx0kw6wak3nihn4w")))) + "1lbvrw6fcjhrm6v71lmnphv4hbdh03czgx3822ckdk6xrvyh54cf")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -14222,13 +14611,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0jr9lp250s9066hh40vxb6c6yhdd8yrnk0zklwylkf3jpbdgl621")))) + "1g4pms5dcr4cdb47gr9kw3mc06v890b38zrsapd4x1cqhgfbgjyg")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -14260,29 +14649,49 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "1946wlw9zvyxdd99rs2rliks54ff5dkibavxd48aj7cqjsjh6b7g")))) + "1wcjmw655k389ph61v3gxjv7gk2q70h25zmdzvd4ggbxg8vh2mp1")))) (build-system r-build-system) (arguments (list #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'make-build-order-reproducible - (lambda _ - (substitute* '("src/SYMPHONY/Cgl/configure.ac" - "src/SYMPHONY/Cgl/configure") - (("for file in `ls \\*/Makefile.in`") - "for file in `ls */Makefile.in | sort`"))))))) + #~(modify-phases %standard-phases + (add-after 'unpack 'make-build-order-reproducible + (lambda _ + (substitute* '("src/SYMPHONY/Cgl/configure.ac" + "src/SYMPHONY/Cgl/configure") + (("for file in `ls \\*/Makefile.in`") + "for file in `ls */Makefile.in | sort`")))) + #$@(if (or (target-aarch64?) + (target-riscv64?)) + #~((add-after 'unpack 'update-config-files + (lambda* (#:key native-inputs inputs #:allow-other-keys) + (for-each + (lambda (location) + (for-each (lambda (file) + (install-file + (search-input-file + (or native-inputs inputs) + (string-append "/bin/" file)) + (dirname location))) + '("config.guess" "config.sub"))) + (find-files "." "config\\.guess"))))) + #~())))) (inputs (list zlib)) (native-inputs - (list pkg-config r-knitr)) + (append + (list pkg-config r-knitr) + (if (or (target-aarch64?) + (target-riscv64?)) + (list config) + '()))) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -14299,14 +14708,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "1pix38lg9snw0jdihh8sifnmckyw1lniwp95r93ca524g6swfc8b")))) + "0j7rfyhpzr8zzyvjyphlfviy07z30nzsqq6isi4l0r4qgaziy1s6")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -14328,14 +14737,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1f0j10wha60vv592vsnv2pcqwz7g2fkld8pnar9rpwwb7qd0wcnf")))) + "1m3awsz8h3gbi82an73kbxcsch2gl737zaanckl1vq2ghymqykrp")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -14345,6 +14754,7 @@ independent of the p-value under the null hypothesis.") r-limma r-markdown r-reshape2 + r-rlang r-rocr r-scales r-shiny @@ -14365,14 +14775,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "06py71xbygfwq55kawh2x340idrf5mmxmnsz5m6lph2ka086dc5v")))) + "1q27zzl570q22nk4xjpnpa674p76hzzvilynx9i6awnzs10zjggn")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -14394,14 +14804,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1z4ddkdd3mzqg0c6l94qmrdwrm7427k5xiwzgkzx43gh1j4911d5")))) + "1h70rm0h711ndj9kz3q10yd9f6npjiwvk9wmkg6w3pdgjni1nrl0")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -14437,14 +14847,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "17iycxxp6jb56ra21546kh2zlrm8by2vrlvsxvx8xmbpk32fb4lp")) + "1k8an0ifcgx54lqzpim3q37y4rhv57i94i46dlpmdyfghqqw0fny")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "MAST"))) @@ -14494,14 +14904,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "0hb2s58xx5cmrn3wlppay7275mln8r5y5dsnvpcps3s6xcab00rm")))) + "0b09mf9fph0mb0zing0prc757d223858q9lj4j3kfpfjpd3jffai")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -14584,16 +14994,16 @@ several functions from the R igraph package.") (define-public r-sangerseqr (package (name "r-sangerseqr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sangerseqR" version)) (sha256 (base32 - "1vggjvxfmmm2gcyfay22wahkib15i164ic148jdps36pxapl6hi3")))) + "01z2b7950yxhv8p73rfmq84bscrlpl956ihfyarnzdq9v9ljzzd9")))) (properties `((upstream-name . "sangerseqR"))) (build-system r-build-system) - (propagated-inputs (list r-biostrings r-shiny r-stringr)) + (propagated-inputs (list r-biostrings r-pwalign r-shiny r-stringr)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/sangerseqR") (synopsis "Tools for Sanger Sequencing data in R") @@ -14700,14 +15110,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0qs0sc47n3p9wmf5cmc39cb30i8pbsyizhr29b3ld197pi1ba5wb")))) + "1aph4phg58f4kpgavrxnn6dzh3lgms8sbjvip4f3gn8xs0p01mbz")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -14726,14 +15136,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "15hzsq8ckw8v8ccz30kia9qr1iymmcszc9z31g5arrx1y816zgbq")))) + "106hawmyln6xj9m2npibb4lkd8qvz60lwjabhn3cpx3908x88ryb")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -14764,14 +15174,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1y0blhh75hb60h9jmvz2naqfzky4zgw5gn81fbj74jfph9y712lp")))) + "1qvnc6cds3avxh1k4z47vb2fih7q8a5b9hccnyrpfks5c0sd6yi0")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light @@ -14808,14 +15218,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.70.0") + (version "2.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1xjfh9lx2cfwzkk61pdarajsa86nzhy3dz7r4zws20pz4xkhwv87")))) + "0rqyv95l8h3s68ywhv3r7hm7j1mbm8prql7p2rlvv4xg31yqmnpl")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -14843,14 +15253,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.44.0") + (version "0.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "15i47b995dqh0dlg60lss5vgj31as3cwhb2z5fqbnknx3lj7s6rl")))) + "0l3n1plz5nvday0a1bm8173mikpfjbzrb1bp8yfvafy7lav4dsyv")))) (build-system r-build-system) (propagated-inputs (list r-base64)) @@ -14864,14 +15274,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0jzxwg28ih1i0f7hal99g60zply0g613b4wrjsbv738cmlsai2kc")))) + "0j4nhdq82dzr19x5w4w4l97clra0z1kk6n24x56hrrj0xlm2cgnm")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) @@ -14888,14 +15298,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0vnm0m9abf8478f7lair58vw1v4mxj8sbmrxcpf8622ygf2na4qc")))) + "08b5d0grmpk5pryffdh6gdafhp1brana353q2kmwhz7x55aq3w68")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -14922,13 +15332,13 @@ studies.") (define-public r-bumpymatrix (package (name "r-bumpymatrix") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BumpyMatrix" version)) (sha256 (base32 - "0ic87fjxwb39nmys09zb6k3ghcx8mmmj9pifljs10449i2lgzl2r")))) + "1f8xa184x6l363psbqn0a5yh16ghm2mciv726aii58bkln5qwkmb")))) (properties `((upstream-name . "BumpyMatrix"))) (build-system r-build-system) (propagated-inputs (list r-iranges r-matrix r-s4vectors)) @@ -14948,13 +15358,13 @@ data in a format that is compatible with two-dimensional containers like the (define-public r-mia (package (name "r-mia") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mia" version)) (sha256 (base32 - "044spfxsf7xijnbh0933cwdkycmg05zsfqhbx5pkfajysh6w5cxp")))) + "1wn2lb7hn4zqqcs2jwavpsbk5kw8d78kxg2yv4jjpikpdz7haa2i")))) (properties `((upstream-name . "mia"))) (build-system r-build-system) (propagated-inputs @@ -14998,13 +15408,13 @@ summarization.") (define-public r-microbiome (package (name "r-microbiome") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "microbiome" version)) (sha256 (base32 - "0xmkwf7v89nwlpjrzqxv87lbsn6za99v7f0yxkgzfk5n6fadrf05")))) + "1azxfydcrxi46j6lykspzchwcj0dpghjia7vfb2bppz9gh8nvk37")))) (properties `((upstream-name . "microbiome"))) (build-system r-build-system) (propagated-inputs @@ -15068,13 +15478,13 @@ experiments.") (define-public r-milor (package (name "r-milor") - (version "1.10.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "1hnvw9x0xwjb0br4yvzkzn73nvm8p3j3wmcw8jrid105j0fz6vcj")))) + "1cb5iw90h6raflgmypd2wc8y4mbsv9g8alshh30k1kjm8vlsw92y")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs @@ -15094,9 +15504,13 @@ experiments.") r-irlba r-limma r-matrix + r-matrixgenerics r-matrixstats + r-numderiv r-patchwork r-rcolorbrewer + r-rcpp + r-rcpparmadillo r-s4vectors r-singlecellexperiment r-stringr @@ -15116,14 +15530,14 @@ model.") (define-public r-minfi (package (name "r-minfi") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "13lldzj68vmmmrp5fi2rfxbchbivaa1scq56hl0v9mxxicw72a0x")))) + "1hk44wddcygh4j7jmj1b0p40hf5qdy1m78x14j19h7z9aq4azdij")))) (build-system r-build-system) (propagated-inputs (list r-beanplot @@ -15167,13 +15581,13 @@ methylation arrays.") (define-public r-missmethyl (package (name "r-missmethyl") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "missMethyl" version)) (sha256 (base32 - "1nv4rm5pbx0s7m5zak3jzmwz4pkf8ghkj0ckdcsnmw3k364ny856")))) + "0fnqa7v6lgld4pdqnvgdzly73aj4a4cn8sgszicxsyn1damxsjiw")))) (properties `((upstream-name . "missMethyl"))) (build-system r-build-system) (propagated-inputs @@ -15217,14 +15631,14 @@ into account multi-gene associated probes.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1vracrvy56kk3hc9midxdaxhad2zf1lspn0zzxjjbsyzx3r0ip0n")))) + "1ms3w43yvy810mr6dml9hqp3kw5jlpr9153kd62gvhjsgikaj3ja")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -15264,17 +15678,22 @@ and Infinium HD arrays are also included.") (define-public r-lefser (package (name "r-lefser") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lefser" version)) (sha256 (base32 - "0aywwinp4wwwa12rq60gpfk5gn28zyimayxakgj4lhfwjk0byz8m")))) + "1qi4q3vijys4q1gfnflvvz8ws3j6f65rpprpgmrkqgiwfn7dvi6g")))) (properties `((upstream-name . "lefser"))) (build-system r-build-system) (propagated-inputs - (list r-coin r-ggplot2 r-mass r-s4vectors r-summarizedexperiment)) + (list r-coin + r-dplyr + r-ggplot2 + r-mass + r-s4vectors + r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/waldronlab/lefser") (synopsis "LEfSE method for microbiome biomarker discovery") @@ -15288,14 +15707,14 @@ to find biomarkers of groups and sub-groups.") (define-public r-lumi (package (name "r-lumi") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0iwkag84w1sc703jcdfx0h799hlchdiqvlps8g8lwmil5b0xlsw5")))) + "04r7dw00yvjrxs0h6mwh79lwp55f5v8s4pgmzcy2fnpb2cdslpzy")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -15327,14 +15746,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1ax5zmby8zw0mgxjd8yhlk4ai0s03zq59qwzqgv8zqlms8yjpvs2")))) + "1la6fwaap7957rrb4cs6w48kjz4hqrw3h39lpps419d4cbnsp5jz")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -15388,14 +15807,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1y595hq40kpsasp74wsbf3ngd2rrriqg65z9y4svcwdygj03pgrz")))) + "1ihski4akl70v6kq03di6w1pz63dx6rxgmyjkm0dv0nhgkmrza22")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -15455,14 +15874,14 @@ are standardized and usable by the accompanying mutossGUI package.") (define-public r-metap (package (name "r-metap") - (version "1.9") + (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "1w4mv7vb94d4pkllvabz9az8sbrbfhigxw4is3j0jzi1pnlyc8kg")))) + "18l86026g5g0pdihw41h7yck1ad5k43bb7as5qih2k5xkr680mzx")))) (build-system r-build-system) (propagated-inputs (list r-lattice @@ -15484,13 +15903,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "06k0jib20nq7zqc5vbgag8v1lbadjlg0idh5jwn5bcjc74dx15vj")))) + "1kgvvvwvj3dgb2wik3y8j44ynda94bi05vvmiwlayrypqprwi1c1")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -15553,14 +15972,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1ibg4cdpbv4ph3y4r90j8zfwr1cy1z33p4bazhzyi2zv3xa1nrq6")))) + "1idil9vkd5risx9ahkagdacnj2g2a11gzsd7wmhg5gjmr77r53ww")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -15593,14 +16012,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.10.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "1vs7x4dc2vrfi2wi300bjr2hl1wwp4v27sgzycr6qv6x2nx9i5xq")))) + "1pc63hk0smcflq4903hvs4pp8r0kzlx08j0m1kxlh14cxwppamyb")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -15618,14 +16037,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.28.1") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "0p8368ia4ib61m1p8apk2d21lhdi62rfg04zl4190w6xv87k49xx")))) + "0985w9b2iw7jbmpymfvqmpzshsy0lvqw7whc1djdnh58lwscnhcq")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -15645,14 +16064,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1b1r7jwilwvl89fw3rqascyhy8wnm8y81lnx85pwjk55ld56jlb1")))) + "1pg9p6982901k08iqpk0cdb9hii3k7bci9gq6an711r8a4iy3lmc")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) @@ -15675,13 +16094,13 @@ the data set is suitable for such analysis.") (define-public r-anota2seq (package (name "r-anota2seq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota2seq" version)) (sha256 - (base32 "0kyxwhj5vq5z4v3x3hfb9ks3h37axqskyj9rzyj2bzsy2yk9hajn")))) + (base32 "140k37wswl4w2136pz9y0z82sphzxmgzgk3cr400kkm39wjn7vxm")))) (properties `((upstream-name . "anota2seq"))) (build-system r-build-system) (propagated-inputs @@ -15711,13 +16130,13 @@ that protein levels remain constant despite fluctuating total mRNA levels.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0hhad9vg43j0yz8fp2w7qdhvdy77yr7anv0fi170042x3piq1q7r")))) + (base32 "1gb15zrv44yn65wns7dk24rp54qv7wafqxgk1q8jnbkq9lp5wj2y")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs @@ -15744,14 +16163,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0sykd4ingpw41615hbr3vw9yd1ks225hdb5qxnhbk4m4wxj814ql")))) + "0nnvqsyrj24h5y8qw8llk9f4jgy0v734k37kcksfcpja17frdyjy")))) (build-system r-build-system) (propagated-inputs (list r-bh @@ -15777,14 +16196,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.28.2") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0kk4l8cxyvcq4cjjnb59zajf4ci0igml13582qqn8123cqkbf8pf")))) + "0hwbl3kcbjpjpdnqcq3ilk2qz3g87nybgv3kyd8fmh935jm66v6s")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -15813,13 +16232,13 @@ data.") (define-public r-enrichedheatmap (package (name "r-enrichedheatmap") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnrichedHeatmap" version)) (sha256 (base32 - "0j87x26qimsx4gi311bm1g9bldwq9r4z3aflxf8p91zlavjbv8zp")))) + "0fmqz9xqs1108a5xxpsc63pplcc0i742r4zdk46p68my28ba2xfq")))) (properties `((upstream-name . "EnrichedHeatmap"))) (build-system r-build-system) (propagated-inputs (list r-circlize @@ -15845,14 +16264,14 @@ correspondance between different data sources.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "05ps96adbn4h8i0mqflzm1h6chjlrmfz6hx393232bhb995jfllx")))) + "0rkp1zidz34h4d02m4jqv509vw0wyrc084hvj3lxr7mb9j7rnq48")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -15888,13 +16307,13 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-classdiscovery (package (name "r-classdiscovery") - (version "3.4.0") + (version "3.4.5") (source (origin (method url-fetch) (uri (cran-uri "ClassDiscovery" version)) (sha256 (base32 - "06l7jvpcdynij05hb0ka33zpg7xdyqyzfzx24s0bnlspp83yc62s")))) + "0k70s7nlmxymxw84174ikqx854hi0pizd9acpr7ky8fb30fyxg31")))) (properties `((upstream-name . "ClassDiscovery"))) (build-system r-build-system) (propagated-inputs @@ -15913,14 +16332,14 @@ attempts to assess their statistical significance.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.10.1") + (version "4.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1jwi9029dy7ga4hv75grib7wdaghslwh4qk5awhgw3192a0qcixf")))) + "0wmfbr4n8a1mg8g3gl9gnqrvq5p6cfay2858fqx7wxpr2q8yynhz")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -15953,13 +16372,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1qnxrdpp75m342q4chwaig413l52giz1h7nd4p9y4b472dqx9hh4")))) + "0pi6qnchh89fhfr50fk4hrrkz1r8gfwjcd7254pgiaxcazv2380a")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -15971,7 +16390,6 @@ profiles (GO and KEGG) of gene and gene clusters.") r-delayedarray r-edger r-hdf5array - r-howmany r-kernlab r-limma r-locfdr @@ -15999,14 +16417,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.82.0") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "0aga7xhx5d1xp09n2im7yqi9y1b3v22l554hi35ahg2lwwvxjiw1")))) + "1m8clkb5rznzv2fwrl59csq8v0ibqwdm4fphq10b8pmyvj880qpn")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -16043,14 +16461,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1mdv0x9lnr0bm96h5f9104nqg2j6cjqvp5prrxx10j0d6464vmkw")))) + "1298mn8yz4i0qqw1i8pd4ym5f65dmyb8wcmpyahzz11na4diybmj")))) (build-system r-build-system) (arguments `(#:phases @@ -16075,14 +16493,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "0iismcsnkyb7m4dwmxw5pyvscj2bhp6zw9hpdb2ff91viynbknq1")))) + "1jn2ikzijd282jl96i9hcvahkc6l2vsd79dxqiz7kwaqcp7hs5z9")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -16099,14 +16517,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1wxkyqyhb3mj04kmaisd09dapywjpc081ihaig5rs04k611ddvhi")))) + "15jcd66brvbjz0p3z2b43ac5k81s3vmcbkwmga0f7f5v53fp8qvw")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -16129,14 +16547,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "19nf3bc0gdwixif50f3bs47a1kw1w1lir1dz4l8zqdp3h8gfmj60")))) + "1yphs36pk2y4qajq24y443yzb2f55b08nl81ylpf65mvxlxd23w2")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -16153,14 +16571,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "16lgbwsgwp77x9a8c3hr1aqhp36skzz72xhbzm0a7w3kagmd8gn6")))) + "08zlg74qryqm238mld876v15a6c71brkz2y1gnbj0rnl1l9f9rbh")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -16177,14 +16595,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0hin5lpwa7cxa862jh3y7d8kq3q9bv76ri08b27jxzyr5p7xwcr2")))) + "19vapjmyd3ly3s2gqa2xfg99gyc6n6lv3c6rpi0ch4hzb7wiinvm")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -16208,14 +16626,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.50.1") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "0sibsmn7ma2imhfn2pn1fvy6hinzlmsczmx944fzg0aj1lpjcdqr")))) + "1wzqpvz49wkbvqij48c3l6vqfvflgic8gzvjdigb1c6mr96l6vgg")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -16229,14 +16647,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0s865nahgm0by2nvjydkjlhkj2sxmrvcrhw7rmm46ld4g10xsrc8")))) + "0aj3kh4c8zk60n6yyh2jblbrvv77071r96m0mrcslqm71dwg9402")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -16277,14 +16695,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "065b4xf5i1bx08494nm3r497bs47s5vf99l2g37nlpvxf7pypvrz")))) + "09lvjb0fa70kcl7mkp4agxv6jcm2ncmnrffav6zmz038imhmvdgm")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) @@ -16302,14 +16720,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "14jcsqb56vn67hjmcjjnwswzbilsarkk8kblc715c7da72q7fzpn")))) + "1d1vfnxj1p4y1074ybmkxv4x3v0i3sn5w3k4bddzlrqbzyb9kkna")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -16356,12 +16774,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "1z72f5f3sh2ak6zjcfc6j6rblkllmdkli0kb57nwxg2j5hrys3xr")))) + (base32 "1m8y76gg80625xz9g9101mfq19glk37p792yzz46807f7g6m8zbh")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -16383,12 +16801,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "02i3hkffhhsbzmn97mv8wc2px5caq9xnp45z0l53dp1jxbmms1h0")))) + (base32 "1mxs83l8yrbcx353h0wpc0lczn1jc0y5vg59y9g9dabk41csib47")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -16403,6 +16821,7 @@ frequency matrices from nine public sources, for multiple organisms.") r-matrixstats r-motifdb r-motifstack + r-pwalign r-rtracklayer r-s4vectors r-stringr @@ -16433,14 +16852,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "10hmqwkysifd59as9zx00p3gj595lwj30ywn9pqb1920q6f5mx2i")) + "15v4z1a0kg4ic411aprzc9b7i2l6c456sfj3jaxy95anw3j3iskj")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "motifStack"))) @@ -16485,14 +16904,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.14.3") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "0rhyfbm5whz4jygar9cqcrfy92h1lyam5wd8d9svhh80f15v53m9")))) + "11sabicr2jm1cc9rdjr6vjqhf0gd9d7k04qlfhcdssvh02f957ia")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -16554,18 +16973,19 @@ these files at JHPCE.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1b53rkhyqnyh5vangh3hy4yccx1yackwbv1pxdimbp840ji6d122")))) + "0licdpzhh6xlma0hnvs4rr4bjr5q4q3g18kipf0is47zj4l91smy")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics + r-biocparallel r-biostrings r-bsgenome r-chippeakanno @@ -16601,14 +17021,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.22.2") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "004483q584530mh5nb28ppa8wllkd639n9yyw309acs2s4rc7saa")))) + "1g3nppcmyj81ia3v9zvsr8jplk8kmvssspvxd94zxh6yb3wrrc6v")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -16706,14 +17126,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "0g086rj06k3wac24zx66dw1yc1bzv25bmlbjbpcpgdcmyjb1i8sf")))) + "1hwawrp0pbrm9xf7fn65nj0q4s49qlnmxfjlmrv5fykyn3i1lhpq")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -16731,14 +17151,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0p7l856a46zzla8brsg901pmh5738j63h7h7rn3da94ny8k417mf")))) + "0mbmw450gdlr46ggvhrgimkbir3lg5dnqsfadn7yyrn7wkcr302f")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -16774,14 +17194,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1d1icbq8i7mwsc7lv9pn4r0vs7azx1lwng5p3ghnray1ygqclbi0")))) + "009ha82393giapvmfw2mi8pmi88f61mr69qj64y5vphcr1smvcl0")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -16793,7 +17213,6 @@ investigation using RNA-seq data.") r-matrix r-mixtools r-r-utils - r-shiny r-summarizedexperiment)) (native-inputs (list r-knitr)) @@ -16815,14 +17234,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.44.0") + (version "4.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0jdi5cn4v5ll43xb3l6sy062snd5p9n2nrryc5aqd2ki18mdmghy")))) + "0qaafn9l9lwrj0yph74g39pghjpg009qz7by64frxg1q0j7ksd2w")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -16854,14 +17273,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "16rdy35wmydcx322pf9j7l7z2mzgrksg1whr8i8xdmdqfnqz3xyb")))) + "0l9wqijwlq1gwybj2fy6jwgq6ja1mvx8yfdv174g5mjflx8nmc06")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -16887,14 +17306,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "022wn0l2wfizlz6d5plkphjsjbmxw2wcvxrzr4vanczjzzyxv5c5")))) + "1qlsjpjxcw96qhrqjlbbinpry9yagn50jc3dnz459dbfvnywr82q")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) @@ -16913,14 +17332,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0s9kjjh1n4a55ycjvcw8ymjcclcj8b35aygx4x1k5af1hf3f7wyb")))) + "0yvn2famnyxkxnw4r1vr0vma6ym9kb343vqgaqkvcp3zpm1fi0p8")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -16952,14 +17371,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "07dxhaywad9ivkrc454hhizfw6a5yvarrc5fp5za2jgsznv408wl")))) + "0908hyji07br1i1zms21a99m3mvi707xj8zbd1w64gzackghabhl")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -17001,14 +17420,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.74.0") + (version "2.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "07ina8w8p5bm382v452i2wpmv90gvgli393lsgp7xy0h9in7h6yg")))) + "01b9b4v19yh42552awl21yyx9vhf9yh9r3l8849x4zwjpnf6anp3")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -17083,14 +17502,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "032qxwgldl1hbgsgb5q3fi7nfg1nx3k0yppqkvim5cif613m1nzq")))) + "0b8afvnczkhmbdg5zna2h5v42zdyvk1zybn9cwcbw22rijiysq99")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17116,14 +17535,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "12d806pyiks5xbvxng4pxn0xqvgs4c526gp2pp2qhdxw0w2m29rj")))) + "1r0dj65i8xg1yb6x7ggb3s40hvzbh596k2g9bxblsbl18z867ydp")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17153,14 +17572,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0pibk6zdqlbm0rxnb95pd94v6lbg67rwmjnpfxizq7wv36pw6kdr")))) + "06d1w5kknm2mb6v6glmyd97n1a33529kgqkkyfbk277ikn45hi9f")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -17221,14 +17640,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "044rz2xsz2v8i9ha20hxn2cwf7wa74p5f25jql8ancp6r3gim9sy")))) + "0ckvnah0ck5z6calgrwk0k3y1nxpcyn41y84kz5bypzr77x6ssj2")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -17245,34 +17664,32 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "4.0.2") + (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "170s260sp880d3rb256189jvfnnmyzf9nxh8bvksng6yp561r8dc")))) + "1cq0jk9xyk5y5mi39zi4gvrpzx65qngfml76bygkhm2lzgy3nddb")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel r-iranges + r-jsonlite r-lattice r-massspecwavelet + r-metabocoreutils r-mscoreutils r-msexperiment r-msfeatures r-msnbase - r-multtest r-mzr - r-plyr r-progress r-protgenerics - r-rann r-rcolorbrewer - r-robustbase r-s4vectors r-spectra r-summarizedexperiment)) @@ -17290,13 +17707,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "04wg645c0gww8mq3vg70gqlwm12dmqxmvk704zvmxcpifhrvpn2b")))) + "1mvr5bpsng87yl1bhd22h45830vw3sla1ysnr29px13if2q5ylmy")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration @@ -17331,14 +17748,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "11g6a2315hllf197ssccybhv6i7p48n7bv2amzpgxs7bs7qg3k9d")))) + "1nwbqagpcs38c66r1arbby76if6pafa4snd6zbp18y71jj8rgvl7")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -17355,14 +17772,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1gq0hxmnnis0g1y6hiphz02dmk3pfjz874xb2bxqw49z7387fwm8")))) + "1px7rgvaj6kks6fp7yqsqjwy4knlzgllzxsiimv8nikmbd57dmi0")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -17389,14 +17806,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "1zkc275sb1qbban7sghqziv3xkg7wjdpghddklv451n7j282k6w1")))) + "0knszrfapndnjzv5948qbfsjamlf7g04yry7yx294l8iwvwip6qv")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -17410,14 +17827,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1ca41q7hxy6p8kvc3qbjplvn40k4jwhf0mb03njifry4xi1xipgy")))) + "1ws4w2kf514adk50sjadgasm7z1xvklcb8s243m12fvlg63dia9i")))) (build-system r-build-system) (inputs (list netpbm perl)) @@ -17442,14 +17859,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "1lp8x9grc07kaz9iy7yc45mk708g9dplsl86fq0ip8rs51c8f31i")))) + "07zlvzfs1c4gcj9hwgqbjhgbrffi301620chrf5lvzly4v7hafwi")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -17475,14 +17892,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "18pnzc51r7l1ypnhavl83r3gy7l91qnqzvl6771zid04g99pk844")))) + "1pgmw41xdq9gd2shc6kawgxz9sw1ydlgs0p35k99k2v50f86r2wy")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -17500,14 +17917,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0dx1psk6f27p1kiw4qwj1nf55gpqgisibzipvlnn5m9q3q8g70gv")))) + "1spwpbx1jjfjcxbwjkl64ccp9k8xs6lm828546qddsgp20y3bhgp")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -17527,14 +17944,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "1plgwi2fmx7bh648fqpzzfqnh84fsgnn5jfcbdf9yia6zzigicql")))) + "1f5y1sza9vm7wqd4mp5g7sypc9kbf9zpl015rbl41wz4y3ai21sb")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17559,14 +17976,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1fd1pfw2ggqb0k2npvibfy8liix57m01cxfxp10shvfbzjjy4wjm")))) + "0wg799c5pzw9g0dbkaa5j4jyccvixqbc8x3xnwk3cgi1dsbhpk34")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -17582,14 +17999,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.10.2") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "00gnnc4yypvjnvh1xq4bzqi34j9i9ld1rnjnb2gsxbhaq5nzq31z")))) + "0jv6hni5x91ssvz4ilhi3y6lylrw4w3xfk8ljmq6gjvyl886sw9f")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -17614,14 +18031,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0p56w6431jg921416dkyiykccvr7alq6x6r1gcx5d9hkcpyncks1")))) + "01rf4w2p1qw4hk9shsdaffyz9g91vffcn4qi1dllsrn3m8pyd1gm")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -17644,14 +18061,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1arwr8gisc5g9bwxlachf3lvxpd2767ahnwdf2p1lidwpfism8l8")))) + "1in3qani4xh5m5zpbny1nbsvh60ahs36bas8hplkdpd8hnhfla56")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments @@ -17680,14 +18097,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "1h44r0frrw54s9nqa539ifg270ggmm634gj9cyhn4z7nhxxh134c")))) + "1i3dg3fn648mzy49m15vbzr3wfnk91xyph5j4sc7ss978l25h17n")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -17723,14 +18140,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "1pxlpwqzbdii0b1swy9vcq905934yfmyqwfx2j3f7n5n4dgglc2q")))) + "0a7k9p08gq537275r7dfzh34ycxx8h4fmac74jimwhsa420793r5")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -17746,7 +18163,7 @@ interpretation.") (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs - (list r-genomicfeatures r-genomicranges r-sgseq)) + (list r-genomicranges r-sgseq r-txdbmaker)) (native-inputs (list r-knitr)) (home-page "https://github.com/fmicompbio/Rhisat2") @@ -17761,14 +18178,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "0695pjvp742qn629kxly4a9crbg6vakdx1ygnyshprjsz6xz2vnn")))) + "116qnp7d7z4a56fv6n55yzrdlmma9gwrw234nmy8iapkn5ms3xky")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -17788,7 +18205,8 @@ index.") r-rsamtools r-rtracklayer r-s4vectors - r-shortread)) + r-shortread + r-txdbmaker)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/QuasR/") @@ -17803,14 +18221,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "0hrhfgv0b9ycw2vmzkpmrv9m9jvvq1n6asnxnrgvzlz81xak84ic")))) + "0szd5ygcvpaiwqss8galxzxpslpfh93rk42s865v0qpv0s9v9x0l")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -17846,14 +18264,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1h5pmd38b9zpbz1nngmk1s0cag4z0vx93yi2n7r85nca9z02cxad")))) + "1l3hkq6n7i9j82aym4ngwablj8jqb70a7y6skx0rjkflya6wbim7")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -17899,14 +18317,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1n17bpzj95hkljvgqpyv92jm4bk1d3j3mdg7106pb3dffvwv52sk")))) + "1y1j5svi52cvixjsn13122kvd0z0c7zfki3p6rr8wjd5w7riiyqw")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -17936,14 +18354,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1k3j1cbapzqk0qr3v4gijskp487xyz2n4lv4kia9y5pmplddxp7v")))) + "0cdkwzrbr6h1dfi3qdh629hi2jlm1hxgq4dvx4z3vc2r6w0c6m11")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17978,14 +18396,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "1j3wkqvha6pzd6d3wm2q4lihn8p9ycw0wmddjqpnqvglb1x7c0f8")))) + "1c56s8lr5cdx27v0rdi4l4h680x6ga9wazf4dj1xkqyliqz65ps5")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -18013,14 +18431,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "16nkxnbsmr0y6km794x2iwbkyrkf0svg6ln3qkqnw0a47a3cbm65")))) + "11cc3nknbckm0v5r7dzgqzw0137w4c08ab10s9svb1y02z45a0qz")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -18054,14 +18472,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0rgfl1kmgf2f0lpj2fzgjvdm5d7swp9wz86jl8q9mydw6z49nxz8")))) + "0nd5b1k0dsxpf93wqx01fgbvk40jcfs7b7w692bsx620lm42ipfg")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -18080,13 +18498,13 @@ and to both short and long sequence reads.") (define-public r-flames (package (name "r-flames") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FLAMES" version)) (sha256 - (base32 "0937zag0h4bvpapld267s5gz36h8zgjrgvbng9m7czdd8w6064ns")))) + (base32 "1fcz0v1vy0q5zmdpawlk4a7fbqd01954p0jby9nbzgbk85hl16mi")))) (properties `((upstream-name . "FLAMES"))) (build-system r-build-system) (arguments @@ -18118,6 +18536,7 @@ and to both short and long sequence reads.") r-ggplot2 r-gridextra r-igraph + r-iranges r-jsonlite r-magrittr r-matrix @@ -18135,7 +18554,11 @@ and to both short and long sequence reads.") r-singlecellexperiment r-stringr r-summarizedexperiment + r-testthat + r-tibble r-tidyr + r-tidyselect + r-txdbmaker r-withr r-zlibbioc)) (native-inputs (list r-knitr)) @@ -18152,13 +18575,13 @@ for manual execution.") (define-public r-flowai (package (name "r-flowai") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowAI" version)) (sha256 (base32 - "1bi13f8q7267lai71sl640w9zgd5a1iln5r4ri2dcskkwb2qxzkz")))) + "1siqza92iak5lz38hbfznqndrmq995ihp6sbam0n2d3mj8vwv9qa")))) (properties `((upstream-name . "flowAI"))) (build-system r-build-system) (propagated-inputs @@ -18218,14 +18641,14 @@ the quality control enables the detection and removal of anomalies.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "11xcz9b4mg3inz8c8f2vckgai67s740qjyynjim4ahf9zd0j7rxs")))) + "0y91kz1n3byadk505432cnlj9dfiw521fgb460d6dmly9s0d9yif")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -18287,14 +18710,14 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.14.1") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1kagik93ddcl3m1i2bqzzlh18lbxywfn3pxmp47p45kayzxzldrf")))) + "0nrj892jihi4fv58si3il42s0vyz3gm4gmb65kidkky63gmsy6iq")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (inputs (list openblas protobuf zlib)) @@ -18312,14 +18735,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.14.2") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "1q47c6pyvcglxs1qga2814b7i84kmm5sncsnl0fhpa9zhx1sjka5")))) + "1zq3qypmzk9ld48r50fmygfdqwwyykii8l0l6gh5bdrdan760bfn")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -18344,14 +18767,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "06n35c5fdkd3l8d5q8a23yslanirwhbf07b4f0zmf9a43zi642bv")))) + "0bkp3q71qj1r2bwfpfriflqklvcqpvh760as7sr489sb18y1xlms")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -18367,14 +18790,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "0z9vgd8v69iq8gv23iiaxrk77j2aq8y2n5k8x9jmxphbm0cm19a0")))) + "1mbq3190nxlzhfb58i7s2f5f9fngda1icnihmyplagh64savlpcn")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs @@ -18397,14 +18820,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.30.2") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0ig23b6apyp35rxxiqd5nw46yjm2784njlafsgw98akhl8ck0g7n")))) + "0z4cfpylj2y3jcljzg15fpjnrhrpzgw49kcprq5sg4cxr96ia2rm")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -18434,14 +18857,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "1hn021p2220a47qzlya8qabc9xgmxk9gcs505m7wx6gx6ysdn418")))) + "1iz4skfs68jg2a59kfaxllf19mp9pk9mpfc2jh3vyas14c3l3zzj")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -18465,14 +18888,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.40.0") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "1xg0hdxh0c1c1wc6d8gcynq8168hi61c3gjdf1223qvqwc39nsby")))) + "1zjjzn10nvbj7lhg9kvp8gr7m2m294pa3zdmajq65ffdynaaavnd")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -18499,14 +18922,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.14.1") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "015yaci2wimax2p772mndmy76qsj307rk4y71r5s8jcb0nwr0qg2")))) + "1vhp43l2iknljy240kzgvckkzbg186nkfdd1m3la9fnf9sqr33z9")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -18528,14 +18951,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.14.3") + (version "4.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "07hnzvzis6425j5kabdrp49wicd331k7kmkk2r7ydchxxlndz3ww")))) + "0k22hifg4sv0xiw983gf1d6y7zkn9072famwj72x47w8vag4i0xz")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -18575,14 +18998,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.14.1") + (version "4.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1q4m6arasq60w0x24qjxbfckfgcpfk428fca733i0q2mgv1mll05")))) + "0q8g3sqmbhinfrb63yhv4lsczjz7pqwhwwsdlz2cg7s8yhp0cj6v")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -18614,14 +19037,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "12b4a65zgswzddkfdyl4j06qp7w9lkxv4h05m4z8hfff8c9x5bls")))) + "08dn7k3jlicj755rwhpw48fmi9via79vd34imaffwdzq3aldi83m")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -18650,19 +19073,18 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0wq9ganas6l2jw8bnajr7vwli35kykpgv2lca4qh79nfgxlicff9")))) + "11kflx3yahl7xjl6x2rgpd4hl5y69qgarzhalmz4qdci7b7ln7kr")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs - (list libxml2 #;zlib - )) + (list libxml2)) (propagated-inputs (list r-bh r-biobase @@ -18695,14 +19117,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "170xz3b4kfsxpqirfz9vk4j8dkdmz4qd0a1nm3yaya1rddpg9m3l")))) + "0xqrp184p00pvzzf6ddmp2r8lpg97bm0q6smjwcrfb8rn4msxmis")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -18731,14 +19153,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.26.0") + (version "6.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0ifi89s611kblncnpvsrbl6sq2zi36binz63njrhya9wkyaxj6pc")))) + "03pdg2hz4wnyigqakb9098ak9ww8fhwypzn006hfad0s042p9wvj")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -18777,18 +19199,19 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "1b3c1wg5xnhh4bdcjls26j6nsp0vx1g5y3grqv7x4ds01vmh3q2w")))) + "15lpn1p2p28lhmzi7svszr0p1zkyaivi69q8pxcrv4lvips38hk4")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs (list r-beanplot + r-clusterr r-collapse r-dosnow r-dplyr @@ -18824,14 +19247,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.20.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "0dp2y85mfn995rvg698xnxlkz1kd8g0byjypxx62cpfldnkrinxl")))) + "1856jnvqacr12j5hnnl4w2abjjd7qvkz7cs8yhbnqpy1896wki0v")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -18846,7 +19269,8 @@ data, to only emphasize the data that actually matters.") r-r-utils r-s4vectors r-summarizedexperiment - r-tibble)) + r-tibble + r-zoo)) (native-inputs (list r-knitr)) (home-page "https://aertslab.org/#scenic") @@ -18866,14 +19290,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "1mcpx785ag0jcsh08df34hx3wp55zd1vggnl3fflkinb78178n38")))) + "05djywxsyfxb26d0clx51q7wmsw3rq56va444d6iy5n7xlhj9m94")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs @@ -18912,14 +19336,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "19vn31w74r45pq5m9pn5db1sz1qg757mghzzs933cdssnqf4m6y5")))) + "0x5ly5hkqli5b67hiaa6ha02damyps7vb4l51p0az1j5fxl39n8r")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -18979,14 +19403,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "098fbrszph5cnh4n9zjhj92sg1bi6h6k57wm2vlaqkq0nab63r63")))) + "0gjnx4645kd7qag7dzs5dp9lhsv6zg5xn6jna3bap4mginl1jvxi")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -19114,14 +19538,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0bsid8qhcqgalqghr2b2592pzm4viyi7wq8h5dmhrrl7gky8l60k")))) + "0ijwyx42saqas52273c63c3yi948bh4pd4lifyqi3zjjs17bj1cg")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs @@ -19138,14 +19562,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "12msc6skvcx4ajk20l71k32rj8lsiafjxwcsrd51kyy5x2yj2v4m")))) + "074c6jg0dyr3hckizpg56f8ij8szj43cx6x5bbw7a01xdjdc70yb")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs @@ -19160,14 +19584,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1ra21qzni9cny52ag9zxi46vb9grabyqjyk01dqqp3r9i0b4999l")))) + "19zlv9aglllsjq3jcnlw994bkanjdq0ib46k7wjsig04cx4apz1v")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -19198,14 +19622,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "03qgiww523kijrkciln3fw3djn20rnvwz2j0i3p518h6fbl7vlpm")) + "1ska6q1800mmsxi6jilpnq4f6cy3vk0nb98gz3ik94lmbv2ram97")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -19256,14 +19680,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "1j80f7k39p23s6fym3nia73g8d1v44hdiv73igcq6fnsllxg40hr")))) + "0fa1dwbk6hdiwg6dmbks7hy4cg3ydyd2sv94cyl0003awhf00nn9")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -19333,14 +19757,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "1y2bk1kla0l72xgdam2l9c0k7584ckdqscqnc184cxvqm6fb335j")))) + "0yr4jfaxs253xg5q0kds8fm97kqacx67pw1c80yx2w79v7nqskgv")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -19380,13 +19804,13 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-tilingarray (package (name "r-tilingarray") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tilingArray" version)) (sha256 (base32 - "01j4wj0mdfrlyhp2alf1xfy78f17x43w9i0wb41ljw6pm313np58")))) + "1408275gvfilc2k8sfsja8bm5fdgnblf2sf5wdd3if51qi61clb0")))) (properties `((upstream-name . "tilingArray"))) (build-system r-build-system) (propagated-inputs @@ -19462,14 +19886,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "01czx88dzqm8qv44kyy1n7b999wgfklxzgvmjh10chf677phnzsr")))) + "14kxlzgy71s8h34galx93q8kalspr1m23brssbr3wha0hxb0ghgd")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -19509,14 +19933,14 @@ populations, splice site strength, conservation, etc.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.32.5") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1yrss51gwg73rlva0xhk34md0cx43h2j4vfk0z2hzchr2r1amzmc")))) + "00hrizpx05jfh7yrab6na10zkahm8ibrbxy4pa4dcldw65klqmn9")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -19588,13 +20012,13 @@ features (e.g. genes, microRNAs).") (define-public r-ucell (package (name "r-ucell") - (version "2.6.2") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "UCell" version)) (sha256 (base32 - "00v4b91f7y3zyndbl4wlfay8wljnqypfc05vrw15yr62d9smd35d")))) + "09r64rrydwgvvvq8f5vzvn7dsh24l9sa1if21wcimrl28ci1g1mv")))) (properties `((upstream-name . "UCell"))) (build-system r-build-system) (propagated-inputs (list r-biocneighbors @@ -19616,6 +20040,32 @@ UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.") (license license:gpl3))) +(define-public r-ucsc-utils + (package + (name "r-ucsc-utils") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "UCSC.utils" version)) + (sha256 + (base32 "0w9f5xd6ryniapbpcrpczn8wimph2154w45cvdgqfa3dv5qy379l")))) + (properties `((upstream-name . "UCSC.utils"))) + (build-system r-build-system) + (propagated-inputs (list r-httr r-jsonlite r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/UCSC.utils") + (synopsis + "Low-level utilities to retrieve data from the UCSC Genome Browser") + (description + "This package provides a set of low-level utilities to retrieve data from the +UCSC Genome Browser. Most functions in the package access the data via the UCSC +REST API but some of them query the UCSC @code{MySQL} server directly. Note +that the primary purpose of the package is to support higher-level +functionalities implemented in downstream packages like @code{GenomeInfoDb} or +txdbmaker.") + (license license:artistic2.0))) + (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") @@ -19643,14 +20093,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0wy7zplypjiqv4wjq0l30xb5xj63fxb7z2wmmfrmzfkbgbm0xyha")))) + "1kasmib3lp68pq5f9qzh38z7gpv8hik536iz16g8a73pc6bcbmzy")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -19692,13 +20142,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "0ll0lksz6nzfj5ivmyrp5w24bhfl083amjpr0m8qlzpdw6k3wi98")))) + "1gpn9z09cfcy2mj7m32xfb2bjjwl01g9qn9nqaivmqbi4k6icrr8")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) @@ -19721,13 +20171,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "1qckqdil1cq8lbrj9di96w9934r1fp48xpmfdwp4f2vw9pjadi1q")))) + "00dcx6kcqq5xcdy7rqgi51cvc20dsgrrki8aicbj1icx0m6601wa")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) @@ -19745,13 +20195,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0cy1f4ki4j7yxc9cws5s17ljd4ac0yxhijms0pm31im81qz2djax")))) + "0jak83dlavhczaa2nqk5g2l0h4grnc9v24bg6v9mjfn6bqhl1s7j")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) @@ -19772,13 +20222,13 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "1rqyjj4lgqxs372qx8p3qx2napww0djh4jz8hzgv86x9r202kk9p")))) + "1h3drjxdmd837hc7l1xk6b4ha39i7bqkb8862h4h6s5rfa7dcc50")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) @@ -19898,14 +20348,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.68.3") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "1a3hq2i1mxf6dpkk82b6y88q5fcjbqpdcxqplkfp5d2slzsqc3jp")))) + "0sglk8q12fvqk6m699v3lajwr1zb8wnrldfv2n8y7jjy2fqcvs19")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments @@ -19934,14 +20384,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1m289q9bs7i7d15g5mzdmzw7yppnqspr8illkya8kxlv1i2sify1")))) + "1fam1k42dwd0gh7dw2gz4yl6bnbkfrw0bd44v8sdpvwwyd1dq1r8")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -19960,14 +20410,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "10inwxl1cmkdp8037wcwkj5wzxsrrcysxfbqhnkh7pzhzvwnzz9h")))) + "0397xg4sj988b0chzfpy23dszpjbdkch59wfynbn4pwyvl0qmp9j")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -19982,14 +20432,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "056zqlql39q44snvx5nzc5snrihpr1kj3jdbpbb401hxi9r64f4r")))) + "148j41mawxvzyal9lfjy7h1gp0w8zwmgc7s32wiqa30qjcc82snx")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -20011,14 +20461,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "0pvj0qgc6hd02g9ppfc610gvfn412rw69rxh43y4dr3n894kdm2i")))) + "02pmxg0ppy1asjscp13kmqyj2phw4q138fj2b3xgmcagwxqzb4bs")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -20037,13 +20487,13 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hybridmtest (package (name "r-hybridmtest") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HybridMTest" version)) (sha256 - (base32 "1jkihcad453d7jqb78fl03yfqz169jz75c40y53569ndp2j4rg71")))) + (base32 "0fh0v29fpwzramqnbxmzpmgiziwswdx38734g2lx303b0blkbv7j")))) (properties `((upstream-name . "HybridMTest"))) (build-system r-build-system) (propagated-inputs @@ -20068,14 +20518,14 @@ then the law of total EBPs.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "16bjjfzcndjfqsywzw2cn551fgqlnll2gi975w0qqxhkh3jssgmi")))) + "12g33rw1qy1ij32k87qrw04pak20p8z04mch9lxjy5yrj5k5x812")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -20090,14 +20540,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1lgfpw9f7095lgk46gdpxq3z52c24xw4ajl7yid3pcgw19bfcgk5")))) + "104xwij9vq5gwq4ml7fnhsp4apcldbgxmhppwklg6zqdfixpmig5")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) @@ -20112,14 +20562,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1pdsxkh9fkgn80f7p21902pb6xp2qafq10p29ifb55qwz8gma2ff")))) + "1ja5j9753rgx61jwkax0mzkxh7ybh3m4ampkr5ikw3afda23wg1z")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -20219,13 +20669,13 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemmineob (package (name "r-chemmineob") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineOB" version)) (sha256 - (base32 "0mfajzwzldmra6g5kni5yw7m2n719456p1vd3hxx2r7l1phdjixi")))) + (base32 "17yvmdg16pb1dmx160n6vcgw3sa1yf40f8yzivdyic3sckn4z4bw")))) (properties `((upstream-name . "ChemmineOB"))) (build-system r-build-system) (arguments @@ -20260,14 +20710,14 @@ add-on package rather than used directly.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1328mwmghflrvir1i3crlq8q36wq60x2an11saabg63hnx4paa81")))) + "1252xy33bgjrd4gh4shrgzklgxry2lf67svzxjra5yckf8am0rdc")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -20303,13 +20753,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "17il9mi1iagl474ia1lz0ajx1wq67jw5famkr1fmjlis8ymw8hnd")))) + (base32 "080src34jwkvbk98pa4ri530l9gi4ibr5mwxib1681np0cfal54g")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs @@ -20332,14 +20782,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "1mm1nzdz9cl8mf33yiyaspqkx4sbqhhs6m9jfgl42fhscrhaxfsi")))) + "0rckhgg73cgz0ppqaywc7nvbnp1is6cyjfa7dn2l32xxrcl57pq6")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -20367,14 +20817,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "1ivclipy2igf8ax7f0pqrcqflcm7h0a8ny6nfa0200vp99an8ymf")))) + "0flj14d8aamr1fzcpd0k7jq5rs0j5dsijpahg066qrnapn5990d0")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -20396,14 +20846,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "1h8j10jx02zsxs6rzids3gy4xchdhgzkifa5grrfbn8faf9ycy2n")))) + "1xymgghgj4r1k9i73zqgava79l0djz945jnl5ad193flv13fpdgs")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -20420,14 +20870,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "0kflwlmyckyivr8xh7fsmpl7jfkq5kavwpkswmvdfqckbd0n9xsc")))) + "0i5jrdzg6zcs1jx0lryq8d467lxi1hvd1x6p74ywwxga88p46zk6")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -20453,14 +20903,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "1m8dy1lmx9m8p5jjk0i7yllb4pvq77kynszk1nz8cc1niz6xs47q")))) + "17ym1y90bz85afanggdjf91a49lz89qmmi2kyhxga0cw056lkdz0")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -20475,13 +20925,13 @@ microarray data.") (define-public r-biocbaseutils (package (name "r-biocbaseutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocBaseUtils" version)) (sha256 (base32 - "189jz8krhv0vdnk47m3cmy95zfg3l328w6dbhg6djvlkca17i275")))) + "0f8bzhpi6xla52sbvpd20sgli7mp5xfk2aqpcv6jkf8s59jsmn54")))) (properties `((upstream-name . "BiocBaseUtils"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -20519,13 +20969,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.38.2") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1pkh7b27ynzpdfvyzqg36jm885r5lf2zw9rppdpj31rcv1640s0k")))) + "0rvr68d5anir7bj913nxwwfj7i3h2dvadcfvjjdbdr3m35wyx1g8")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -20552,14 +21002,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1yy0bwvfa5b531jvmbiwrd4xg8cdvrgwr8l6bxasrh6yrbv8drml")))) + "0ji6pa8wfj57drpnp03vgas1pird84g15nnp6469jmx773izhfq0")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -20574,13 +21024,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "17pkdi3vn62pw1nzmgz0i45czynqjchq078ij8v1xvflg6lf7flw")))) + "1vm9wj4hzzjivdi6rnxyhxwqscdvbmc45w9zq17h3r53qnva530x")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -20598,13 +21048,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0fpka47shrxcbc1k057f5zv79406daic0y34v8p5lsvxbgzh0m8b")))) + "10j9s50ppfx8r752wkabls0n4gxp17z7dnaf352f3dcdbfa8ijh5")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -20627,14 +21077,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1prl24sg5l142155z3iaxrvig2wv2xqajq02nj30jjjih4p4936w")))) + "0mj1aqxyp84mn5m0fwk9lijysy594hhga3kv4mddv45vqxdsr08h")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -20660,13 +21110,13 @@ access.") (define-public r-experimenthubdata (package (name "r-experimenthubdata") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHubData" version)) (sha256 - (base32 "0msg3wpz1ppvwc4dsm9bz9h4y4hz67xr1xwp4vv4100sg0i5v9jn")))) + (base32 "1adm3b0nacbdi4x5z71iiif9d876m3ip6crhbbr2hw4mbk6is7qn")))) (properties `((upstream-name . "ExperimentHubData"))) (build-system r-build-system) (propagated-inputs (list r-annotationhubdata @@ -20688,14 +21138,14 @@ db and resource files to AWS S3 buckets.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "15ibdbpj7vqypxfnp2w06w9lync11z3azzss6s97xhadkgsbw4vq")))) + "1vmck9ridjjk22477sv8wx0x7n5irrsaf6nsh9lm3krk4i3iv715")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -20715,14 +21165,14 @@ db and resource files to AWS S3 buckets.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0dmhqymh800mljcpdf817nbyg20czp8y9bg13p3r4bfj6axxckch")))) + "07sfcc2cd68qmspcm4ypp3cg05d20fbpwiz5ik4lqsa0hw0j2dhw")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -20752,14 +21202,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.22.2") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "0yx32yj9bw78nhbv1yvgs26sxdmnava1a89g9hs4ai26c1hy150s")))) + "0h4cr7lrmbyx7kdj81s7ff75svr01rvzn54svqi93vjilawmpbm3")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -20798,14 +21248,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "0710dl05hs590fimp3dhg5hzvk6s79i0kwk6w6sj59pcawx2l6il")))) + "0jpi51f9cv3sv4l69974bba8c8k0inb6zxviv7i907ldaiiblr07")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -20825,14 +21275,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0swi6xiads31xcndc2cfzh0ivdl0wc88s83s1p1gxh51rgmgkb14")) + "1nbzr1yjz65r0y8c312hnvagnc1pdgda4v6sxbpvlkl3z93jsy6x")) (snippet '(for-each delete-file '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js" @@ -20939,14 +21389,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1qmi6b0hrfzj7ixcbxlsxyy3qg7d2qrq8jcjrjrgfyrgcfws46qd")))) + "1r1if1k7qgni3dk7gsl4vcyvd6hnhx94rcq5yi9w7dvyyrbvnwwa")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -20977,14 +21427,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "0mh7lsiprshq56ns3b8pbv1j1mjcbdzqydvli0ynmvf5smn2j4m5")))) + "1gw0lmdhkzp5ar54yv9jagqmpxp7j9ajfmdqb2y2qrnhh39hymzs")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -21010,14 +21460,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "0ngpysb89wag4wvcq83ddjxhy1zhl32b2fy2fg5laa4g8xfrqaxz")))) + "1yxr5df1y8v5c9imh27j86s7g9wjvi51j2wyn8jgma875mad41hq")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -21032,14 +21482,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "18rzv4kldjmm2zvz9pzrpspig2hy6mcvb45hgmw49ba4jdcxh31s")))) + "04a1fvwgqxzf7992lyh9qzz2z2fgmfwfjvpw5xr21pcrpas57l2r")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -21078,14 +21528,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "09fvmfiavawfwbxaj1585l2n00fibx9z3r17dv06hc6b40a1sa12")))) + "0sszyfnnzzn5xhs39zgkzr7f3da820nxr6qaw68wknblgmyyddi8")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs @@ -21124,14 +21574,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "0q6npc5pglmhzm9270pi11kbp5wg3ncvflp4rhv3w778qza2zlk1")))) + "1h3zxb3m68lq37g25zqxpmk2c9yrdhydyhh7ad2d30hif73qiacm")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -21157,14 +21607,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "0fz66bchf41jzgabs1s8drpi3f7g27lid5g50lxwh6ph3i02cpaw")))) + "16bblkxp8pj7qaxfzmp30lfj8vy13d3q8cf5y0g40lk4rbldx3bz")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -21280,14 +21730,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "15fy3vwnjx6rwrkhbwxyvdykkfdis8c0m18x6y7irvyij9lm6x1y")))) + "1cd91iakbpf2hjysc44sqqrah63cgq4fz3n8j81virfwl3ir95xm")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -21301,13 +21751,13 @@ routines.") (define-public r-s4arrays (package (name "r-s4arrays") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Arrays" version)) (sha256 (base32 - "1z6kcgjb5fzslr02vmsvchbilrhwpgh1ghk1zmlq0h0lyzncaapd")))) + "1k7nxvlj7cjkhm0i30a93x9ll66mpci19l93qjs2540fvbp9n86y")))) (properties `((upstream-name . "S4Arrays"))) (build-system r-build-system) (propagated-inputs @@ -21338,13 +21788,13 @@ array-like semantic. It also provides: (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.40.2") + (version "0.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "10lryil0psfyal0006rbhj0dbxyn8f7mpp11h758zc217cxsdnac")))) + "0aq0j70sl8a42gc1abxdwdy74mi9k4krz56yrbpwqv78x42cjjm9")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -21406,14 +21856,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "03l6yr76inv4fivy10g0h2qafgywrcjnnhs694lwqz1y6r0gm1sy")))) + "09i174a867vqyb6677sj88lk6bpfc4ajsmjgjkd7f7q66j46q655")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -21444,13 +21894,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "04vl4cp0izghm7h4xk7x48lqkq0dpl47dkd068lva33jygwwpvcz")))) + "02lzx8whxd3z4k0saf0vaq4np8lag00nkp3hd6da1w91vczs1kjl")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (propagated-inputs @@ -21480,13 +21930,13 @@ working with Salmon and Alevin quantification files.") (define-public r-fithic (package (name "r-fithic") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0ygcq3xi55swsmysn539cr3m504rfb6zm30w747pa46r63dfjda7")))) + "107hm9k9wfr34fradldmjym2bzxb6qx8109p4a7xrqkiya0hmwwa")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -21504,13 +21954,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "16svq29fm9xl3rl9v6lyxf564manvp8ryxj1mbxc4pb360wmi780")))) + "0nxk3rdfw78bwyxjd3bbm093i8hqyk63rz0fvx3fi04qpa1fv39r")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -21533,18 +21983,18 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "17cjjlgbp5kj0cpjm6915wy4cm6h5wl6d59j4na1s6kvgxx95qd0")))) + "0j8rz99qw1rism3f5cv7rksccijmnchrkw7s9shxk0528f6dj6p1")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs - (list zlib)) + (list)) (propagated-inputs (list r-biocgenerics r-delayedarray @@ -21565,14 +22015,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0b2g57dxvzmnq6dig4dz7cy8lpy3q7fih5q643i5xjcds2cj6lk5")) + "0q4ix3nzr69pmwm6vdna51yxlqi8frch0xyv6wmiy35n67d4fcab")) (modules '((guix build utils))) (snippet '(begin @@ -21646,14 +22096,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1kz8jn3kaqrhvk1dd92l7w45mmwabcqb0508fv4i4w307ja8xk2l")))) + "0gvxz9w2mi8scqyyhhnrasscs7hwvxxlqvh7j9m6akpi8qq91v6y")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp r-sparsearray)) @@ -21669,13 +22119,13 @@ matrices.") (define-public r-beadarray (package (name "r-beadarray") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beadarray" version)) (sha256 (base32 - "0qwka7549mlv2x80bjrzdsy4a6h35yxrhj2cxss9aigwsbjb7sjr")))) + "0yda6maj985k374bh6zkrs8qffw1jrz9gc3mja07ibyn4pvzkclq")))) (properties `((upstream-name . "beadarray"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -21722,13 +22172,13 @@ performs copy number calculations and reports.") (define-public r-beaddatapackr (package (name "r-beaddatapackr") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BeadDataPackR" version)) (sha256 (base32 - "0sfpdpw6qqffzb9skzx9w1ggcixc3wry9c6f2kwpsykbdsnk90xz")))) + "0wz3prri0mfjczmb432faxfjc99wg4lq26l3a60rmxyxq8mcnpkv")))) (properties `((upstream-name . "BeadDataPackR"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -21745,13 +22195,13 @@ decompression of raw bead-level data from the Illumina BeadArray platform.") (define-public r-cner (package (name "r-cner") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "0kpz15l3yz26s2kskxk4093313c7vwi131y24wbpcdahicpqys2m")))) + (base32 "19kfh7p8zlb1nbwpsj6i1b7pqy829dij7n7iavznhxw44cmif6sv")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) @@ -21768,6 +22218,7 @@ decompression of raw bead-level data from the Illumina BeadArray platform.") r-iranges r-keggrest r-powerlaw + r-pwalign r-r-utils r-readr r-reshape2 @@ -21793,14 +22244,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "18msr889nygk1c3wsjxc9bv989zakkl9f1h2a6cnfy8rxhbxpvwq")))) + "0bmmsgmx7159bdrflykkis0v4z1ixwlnmw1kx0y0kw15lw3cjnsh")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -21817,6 +22268,7 @@ advanced visualization of sets of conserved noncoding elements.") r-genomicranges r-gtools r-iranges + r-pwalign r-rsqlite r-rtracklayer r-s4vectors @@ -21839,13 +22291,13 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "025wlqnx13ldzyrf72mrfj492d62i4xyjbhpmgavgld0jwfmr3ga")))) + (base32 "0c2sf8l1wfgz3nh9ccm10y9wwh7rv55r09awavqlrr9glcbblp32")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs @@ -21868,14 +22320,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "13kkg9xpyvgqpsaz5f96pd43i8a45jrbnzqmax793zkv4ai8p16j")))) + "1wpvdg5x51cbzpqa4s2s0zl9h7fsrsp87mxxlhxs65zx6yyfj2xl")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -21902,13 +22354,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1vy650625b9b2dgnkgh5h0kw5bkdvfin133091asf1nw4jgnn1vx")))) + (base32 "092y1x1sbqvjrwmr7sv2r5216wbwwc4lk6kwn57fnvvdnc0hc3sv")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -21949,14 +22401,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0q44n97mly1ldh52r0sb1jwhz8bn4n7sfw99qs5h4s44w9s0fry4")))) + "09sbk0r9g55x8fbvv5rbrygdw3km4bbrj9x0abqwld2nxnxq1q3n")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -21977,13 +22429,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "2.4.1") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0zlv45diasff5ipxp99dddswclrzzdcmkqp278fm2cj7aibvb3sd")))) + (base32 "0l33bsi1zfj7f4hzlivhh89phhx0qscrwd08c28mqvcyp91mhq16")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs @@ -22009,14 +22461,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "090arfacfs09x7g60qxz4bj2gqb97y3kmhafywkgnrj7pz1z0qzq")))) + "1cja56k5y5vi1x0jdxaxvh13fc2lzh8g30gp294pz6p61prrf3ws")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -22044,13 +22496,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "06a4nxxsgmi435m06ir401w4fbrh0xdgh6mkv3i7vw001yrbrfcx")))) + "096crwk5a9i7h2pykyi6vgnrnxas9wdz5dx920yh74smyh527jiq")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -22088,14 +22540,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.30.2") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "06b454ydd8n8xbswxf1hacm3g2nr0ik0gg08pr7crgnsm0r3vpvs")))) + "0s1y2q4v596wxh8p5sr43mk9cnsc4kg36ld7vx71hbn3hwscqaa1")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -22131,13 +22583,13 @@ variable and significantly correlated genes.") (define-public r-sparsearray (package (name "r-sparsearray") - (version "1.2.4") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SparseArray" version)) (sha256 - (base32 "0gz1j8g020bp88i5idrhj9qrixgar3wvxxna46ds60q6d8lsn4vi")))) + (base32 "1kik0g208x58kycc9njp28fiacia2i8f1m5ljz9pfyw6mn1cspwm")))) (properties `((upstream-name . "SparseArray"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -22168,14 +22620,14 @@ in the @code{matrixStats} package from CRAN.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0r2jxwha2xjp8iy7al85s5vib4xvl47gmlbbvvjj4wnz2gfzic9r")))) + "04hk9r6sh83dyxm2j7jdcj0m4g74ln218j21rs71c2gg6mrkmlgf")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -22193,13 +22645,13 @@ data in the column sparse format.") (define-public r-spatialexperiment (package (name "r-spatialexperiment") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SpatialExperiment" version)) (sha256 (base32 - "1s42jzq95f662h39zmbf06qmrrglbch8sgygpnwqblrjbrqgm7n4")))) + "0f04azs6wscibcpbmc1m21wjswmgr2b8gvd1n2yavya1li0xxm4r")))) (properties `((upstream-name . "SpatialExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biocfilecache @@ -22224,14 +22676,14 @@ Visium platform.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "18r5rfx46lac0kaakha4gqs4pj8vb39z0908gpclmp3ajca4hzb1")))) + "1cqf6y0f18469v1jgfvdjnskkc89i3sfg79axxqcwa33mfjj736s")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -22259,14 +22711,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "0l6rdkpg89pds3n5y4khvaifgbvm38n0vlpi15h97rnk8x461rsz")))) + "18m6qbj43p6zsrsdp7in15z3hcnqzqcxbk24qvbq7328rrhdk84a")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -22288,13 +22740,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "0vpsc7i6j2skn6wba178iy406yvd4p8xf3lq2qmm2inimxl983cs")))) + (base32 "1prn45vlacj69388psimy0w05a84y8sdry6678pz611sd0ks1gka")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs @@ -22318,14 +22770,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "0bn2jknvj2ag1yv67kjqr7gsq771rmqv3my9njjkwcc9nzrxzhbp")))) + "0ppsldpn3vbliimjvnxadn61crck45j581dw4lc5f3w1vy5vs44h")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs @@ -22351,14 +22803,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0xxjkr3x654n61q2yda09cghvssyx4ml9g22gfzfhbzjp8j7pm2c")))) + "1fzw36181rw7z62qggq7j22qhq8zrblpmv8qkqlfg140ywvwv08a")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -22374,14 +22826,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "0dif4yvm9hfrnamjph5xa9cbf41f2v8lbgyr88f11alwwbf0dg69")))) + "0fadwss9z4bfgkhrrqv322j8x40l5cl4ib85057h4fn03qdijqhq")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -22403,14 +22855,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "1zfb4b88j0ksvsxq8kgrjs0xqlr10yzvr772r8nhl797qzwdag08")))) + "168yfkqlg6af8ndlw4wzb9adg4lgkgkjbsi4a435ks0n4c9dycb7")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -22465,14 +22917,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0vapjfzhwlzxd049fsr00jd7lp48h9qwd95m2sqhqryqz1vsi7hz")))) + "0f4y0szdqhg63vaw7f1lmgzb72bhfpz20g9naq84s8bq2xsf8cy6")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -22505,14 +22957,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1chs58ifpwz4crcl5ymnb8ah3wf2jrn9lla3ljsywqiqn0r3i1am")))) + "0g6h1h8azy79pzm0g8967f58gp33nl8866b285ybq6501nj8pb1p")))) (build-system r-build-system) (arguments `(#:phases @@ -22673,14 +23125,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.46.1") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0an8hd2g2hp3p1vfsmxq77fm71xlf5g73j4w5mcy28x1aj073zxf")))) + "07w37kq6zx99z980if4brwmw25vjgvxd8xj3l1893idbdf70py0p")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -22722,14 +23174,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "028n8v1pgkr1q5s9wslql8ayk1cbx6a9a2rjka9pdwz6rq1iyagy")))) + "08b70drlasws3h9d8iznaxxp0qf4n1fi943m4yngy1c65h3a30rc")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -22756,13 +23208,13 @@ EMBL-EBI GWAS catalog.") (define-public r-gwastools (package (name "r-gwastools") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GWASTools" version)) (sha256 (base32 - "1rjgdcw65zmmg5dy9mdaz720nvqk03bfsfvkdsa1wwhvlnxmscp8")))) + "013qv2wac90s1rv992bwzq4diqfq7r18qk7gcifmi22samplpnw4")))) (properties `((upstream-name . "GWASTools"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -22788,13 +23240,13 @@ annotation, and functions for GWAS data cleaning and analysis.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0i9iqr87mqih0rkbjx3wa383x4yfyzpcb0b0xzairbqgygvcq4kl")))) + (base32 "0lffqbvwmfjbw5ymxr969znvb53hbqfgq1zwffsc768rv3h4c6p7")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs @@ -22812,14 +23264,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "1caxzc99kga2c90m2ydmnvcd8lfp0igmmickpl0ikrhwjlbfnc0p")))) + "1l4l35bpz4j1iliy9dj09qq8r4nimd9pcm0gm4g3sb4325z6cd5h")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -22934,13 +23386,13 @@ other functional sequencing data.") (define-public r-parody (package (name "r-parody") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "parody" version)) (sha256 - (base32 "05mhbkhyh92bwmx37fpviprr9i4z0i6g24l71zk17gq0f8hwb4jj")))) + (base32 "0k2gc8p9dk7j21n6hxdqjna09m6cggx47spkmxkqvwqm97mwqzrp")))) (properties `((upstream-name . "parody"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -22955,13 +23407,13 @@ methods based on resistant statistics.") (define-public r-pathview (package (name "r-pathview") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "17kl7yvpjhsb52kz1pw3jnk6s480lnpvvh9rragndixsl8bkmqmc")))) + (base32 "1papw23dhhkqmm864dc3xm028xm0ywc6sjcm7xk93f2j7yj65x0v")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -23017,13 +23469,13 @@ segmented data for individual and multiple arrays.") (define-public r-snprelate (package (name "r-snprelate") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SNPRelate" version)) (sha256 (base32 - "0d15r7qwwrr6m9saikx4x6hj56kb3p2w3v1awkgm3wfqfgdf1pin")))) + "0znk9vvnahkypmkrx82r1ryp41xr675b4ddpgx0nl3708xhncz5f")))) (properties `((upstream-name . "SNPRelate"))) (build-system r-build-system) (propagated-inputs (list r-gdsfmt)) @@ -23052,14 +23504,14 @@ whole-genome and whole-exome variant data.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0a4kyv93ljv7n62ghx66l81q6sw24llr0998nsalidyws1wldbyr")))) + "160pl3dy7v89i90x262hxqgipas4pyim600l6m50g3c03vm5in03")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) @@ -23076,14 +23528,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1yykcqxp8y7by4jgh6dfl25m0pnghj36qy21990n2sdfv1kpg2x6")))) + "0swkjq50p3ak0ddyg7pqg37fivdpr3v5jpakn38sk5i5ycn3qf3g")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -23114,14 +23566,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "09i6j8dcmzvd9gh9629523hw0hbng18jdqw5gf1r31ck8m8wwmnc")))) + "1agr3n787dqly09wy274v9dg52vdb0n0z3gdh2zsbklkbmayqxqy")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -23167,14 +23619,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "1r3qz6y97zhp7swcv2ls1h6cz0l66y5ap00wx9wlqxv14sljd135")))) + "0x3avbqf0ipmb70szf2chhbdg14ba2hwhyyz0wd66c1qwfk6aj9v")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -23201,17 +23653,17 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0g9d4q6vh2ys1la15fqgbc4ckfbjbzzaqa49x9liqrhpnrp59vc3")))) + "0394x1x81hgibvqb1dbrm8h3y72xfv9xi9fgqghjgnrw6farrkdk")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) - (inputs (list megadepth)) + (inputs (list)) (propagated-inputs (list r-cmdfun r-dplyr @@ -23234,14 +23686,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "1a8jmlx17qcx9qzcaxbnlk6qji6hqxcnzmr8zvar9jrfhx0cv9x1")))) + "17i93h0q1fwl8wymmlgjsh8hbnaws6baf4jid5k579aap32zb5ha")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -23304,14 +23756,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1ahip21wihwg9yhq0ya1cyzd2cq423hz9pd6iql6y3yhld4j5rnn")))) + "1jbb93inv7z0i8b1jr6ax98gqkqn73m86hj61irgyysk7hn4bbg6")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -23338,14 +23790,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "18p5r67ppkw8wxxkrj76q68ljlhdbhar5hc89ffdsgr3zzdyk875")))) + "0660rc8b4vkic4dbf64wkky68f0hk92ip52x7gihvv203cj9fin4")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs @@ -23362,14 +23814,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.60.0") + (version "3.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "17v2x7cyw74h0zfsz33pyl1kqk976pdzw7mrgprz9l7w5120niw5")))) + "1627gqqk8v3sx5kgm7z3wkimbz7dpf37ljrmvwbd4z6ag2yiirbj")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -23384,14 +23836,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1k61aka780xmf1vhqm6zvzjr2626hv71f8gp1s81az939crxlrqd")))) + "0jfczma8sh9dza105v306xr371f8mndndm6kw3ydgqlxd8zk3a6l")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) @@ -23409,14 +23861,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "191b8qhldxvsw09l2c0ffc1ldmx0mqxgsx6m074f28l01d3c1d9q")))) + "03958xwwywsl5ql6ss1rbkklk49ksgvbp4nqcmmqhn1hiwwn8rvi")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) @@ -23433,13 +23885,13 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basic4cseq (package (name "r-basic4cseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Basic4Cseq" version)) (sha256 - (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4")))) + (base32 "0ipxhdsqa8q49d2i17kvwyn6w2rpyl9jmq9bhch7cjawykjla5kf")))) (properties `((upstream-name . "Basic4Cseq"))) (build-system r-build-system) (propagated-inputs @@ -23464,13 +23916,13 @@ approach and a multi-scale contact profile.") (define-public r-basics (package (name "r-basics") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BASiCS" version)) (sha256 - (base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8")))) + (base32 "0rcc8na0nravf2687bcvbaklwa0z8b43lvdy0nf9xvfrfpr1zjnw")))) (properties `((upstream-name . "BASiCS"))) (build-system r-build-system) (propagated-inputs @@ -23514,13 +23966,13 @@ pre-specified groups of cells.") (define-public r-basicstarrseq (package (name "r-basicstarrseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BasicSTARRseq" version)) (sha256 - (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa")))) + (base32 "1w69qc81pj3c4gq158ag59wbpm2aaiqmnnb79m0h7dlsnf964cjv")))) (properties `((upstream-name . "BasicSTARRseq"))) (build-system r-build-system) (propagated-inputs @@ -23549,14 +24001,14 @@ input.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "19m4h90rkk6mizllkih2xmxag8nb45qss3vydkkyj62s5zjhfh27")))) + "04amc13h4ghy1zr9wkdl42wgicxz5s2iwsspxvvi18acm06nzgfh")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -23573,14 +24025,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "0hmx2jpfmjv87mp99mzbbzg00m6arpkpc5prkfav065iwjqbqnpd")))) + "1jhaar524z4ly8d4c7nyjn094m4sgz4vhh8qljd2yvs30xxs0jin")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -23599,13 +24051,13 @@ Python environments in a single R session.") (define-public r-bayesknockdown (package (name "r-bayesknockdown") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BayesKnockdown" version)) (sha256 - (base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8")))) + (base32 "05plmh36s00jh4ckcgvi2s9ypa8mxlsy23mzysazbfsr022x3vqa")))) (properties `((upstream-name . "BayesKnockdown"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -23623,13 +24075,13 @@ targets. It can also be used for differential expression/2-class data.") (define-public r-bayesspace (package (name "r-bayesspace") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BayesSpace" version)) (sha256 - (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105")))) + (base32 "0q1haqsyc61yxz1n197sv3s6csjpns4fi288kf58nnf5jgdwnyx5")))) (properties `((upstream-name . "BayesSpace"))) (build-system r-build-system) (propagated-inputs @@ -23670,13 +24122,13 @@ features such as gene expression or cell type composition can be imputed.") (define-public r-baynorm (package (name "r-baynorm") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bayNorm" version)) (sha256 - (base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq")))) + (base32 "0b05446vcqxr7smxyhmvl6rxlckzzgqhf5v1059657kihhscqr7s")))) (properties `((upstream-name . "bayNorm"))) (build-system r-build-system) (propagated-inputs @@ -23709,13 +24161,13 @@ posterior (3D array).") (define-public r-bbcanalyzer (package (name "r-bbcanalyzer") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BBCAnalyzer" version)) (sha256 - (base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1")))) + (base32 "16zm6fix5f5277dkdaxyxl1q1n52960ma3vw8001a5bjxhic58rn")))) (properties `((upstream-name . "BBCAnalyzer"))) (build-system r-build-system) (propagated-inputs @@ -23739,13 +24191,13 @@ included in the plots.") (define-public r-bcrank (package (name "r-bcrank") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BCRANK" version)) (sha256 - (base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9")))) + (base32 "0ydajrbggvqakdf01pq5mqi1v3slz00irpbx4s9fmxvci9ganwp7")))) (properties `((upstream-name . "BCRANK"))) (build-system r-build-system) (propagated-inputs (list r-biostrings)) @@ -23759,14 +24211,14 @@ transcription factor binding consensus by heuristic search.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "0lxcsw70ib8wvkp3ii1l8vd4g2ddhj6g0x22dwcmwacr2myk3bg8")))) + "1f09vw5qjxyirz5xbvnnjlwxg7z0i0y8yry49d1gyx0spyhzl7sp")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -23823,14 +24275,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "18w062s0wwdisl6a9a79in6h4052x3janinc5isip0x6p9g9d9bk")))) + "0zkd6505q0myc5l9d69i1fvfhcrjqxkv208p84zr5p7xi8jmg3dw")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -23869,14 +24321,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "1ccnrz8rkg533kil3sc8wnjqsmiyrpqqmk7av7ls01avglcjdjq1")))) + "0jys0nmp833ax96vfdh1adikpyapr5gkmldx5kvv5bqiqc8aipzb")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs @@ -23898,14 +24350,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "16finp6q89n6x5q2v1khpfp5ys7d4dvlh3kacv5qbdh1bsb3fpax")))) + "1wi6acw51q48v149l72b2pp0iyjrwq1bbmr53y3m609xfadg4qim")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -23918,14 +24370,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "04ckv1y5iqawd0dvnn0bbpnmyys0ivcmf0my6dld3hib3idjzwfx")))) + "0dfdksk3nc6pzw21sbd4cdqr05489qh4984wv0f906hyb52waxk2")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -23940,14 +24392,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.42.2") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "1imni8lpjzf53w2q34ql0j9rwq6drbzxvs0nhzf6s172iqym2hq3")))) + "1wk0qagx9s2lxykc1fp7l35kl6q17lqy6x4fl2c57v3wa11f47mi")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (arguments @@ -23974,14 +24426,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.10.3") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "1vf3kq4lj4alvwzf0wl09lxb0ky6q0x94ajmrnihlj5saliqb73c")))) + "02jqlpd31mhxbvksj7ny34f6dv8skkkr76lkiaj5gm078kfr0zx5")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -24030,14 +24482,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "122rj6rg4j9q9brhxyrbkc91fml3davk044s2yxwyjnwn2yjw0bq")))) + "0lpqvm0cx7pnb99jh7na49x10w2v04xydiwxn9l41ngxysp8v0h6")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -24114,14 +24566,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "15kmg102259h2yl3b6ncq2p545kdac4hk4kwm1s5492y5rg7qkla")))) + "14yrqf5wl9r596zvlpf4y48nykg0gwzlxfgi3kdx0i5pfgvi43vk")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs @@ -24170,14 +24622,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "0h796sxv7fvwx9m8ikamf3bvaac7rimp33lv1j3ngsjifigdkvfy")))) + "06kixhzkrzxyic44kdmqrv19v2c4a7sri8cbhbvww8km4n5l39sf")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs @@ -24212,14 +24664,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "0afpzr52mf2ab7gr9swdf6609787ymw8s8wksis0d4ap0y0wdgg0")))) + "1b7a9ryl4lz6qy2pni3k9bk6hdf147s3m7fx0icg6fkgi0ymssyx")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -24258,13 +24710,13 @@ visualizing bisulfite sequencing data.") (define-public r-dada2 (package (name "r-dada2") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dada2" version)) (sha256 (base32 - "0rvnwbknvwksm50f4rw9965gnhy13rjgdfvv428xsqixgkkkyrf6")))) + "1ac0nb5bcmzmqpi3vjdmns6xqq3ar61dks6qb3c0k48c78w88b7b")))) (properties `((upstream-name . "dada2"))) (build-system r-build-system) (propagated-inputs @@ -24295,14 +24747,14 @@ fragments by exact matching.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "10ps9k5cp2adpx91g23gc9hl1qzzax5w1mxjcjaii7knkh70cz3p")))) + "0p7xpyl1wni17y7qsincpvllaynxwppmyg6hsza51srs4dhr7sf1")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -24341,13 +24793,13 @@ interest on transformed methylation proportions.") (define-public r-omicade4 (package (name "r-omicade4") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "0i4ln95ayl1irr8sr3639x35ilysdi663kksw7g93q1ry91yav8r")))) + "18gp8qpmnbc5yjqyvvwvmrdybvm6zddc0r8bfglxz5wg4a91h4wk")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) @@ -24360,13 +24812,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.10.1") + (version "3.11.10") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "1wbzb4kh7bzsvixr3vxzih9rfkpjx00f33i0yl0dqj0yixnrghwr")))) + (base32 "1izy0ycrvac0k67dxq8879rbdghkrczd3s2g5v607js7bmfxybjz")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -24417,14 +24869,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "1q90p14qj5plz6cbvwxq875y29in6jg7adyni5wd33pf9i4gsxzi")))) + "15bisrcgyiv9ndfvgm0p4igyr4jwsf68ccis1nf1hi9x291k7m6y")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -24469,13 +24921,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.30.4") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0br0bgcvxxfy1vclfc8i20b0bsb7rcchwfdx7lkw4f2aqxny8ja8")))) + (base32 "1br2dxi5rvl8z5myrnj4dnfh8xgksrqjyy0fsqh3vjspifvis4ih")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -24524,13 +24976,13 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "1dawkp681pz9hf7fp2nag9pcfxx5rq0z4j9czlalf0sylsjbirkd")))) + "11928pcd8xzmll28m0ihi3rasc4w1i0fshn4bh9n2lyigkr5ayi4")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs @@ -24563,14 +25015,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.20.3") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0hlx5kvhspc62p68gz53n0scwji3zvfv915fm8rzw3l8h2hjh3y7")))) + "11fxd0ybp3d8l12k1f06qhnmq9s52d5g1fzc4rj20gafyy9fz496")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs @@ -24588,6 +25040,7 @@ embeddings and functions to build new reference.") r-s4vectors r-summarizedexperiment r-tibble + r-txdbmaker r-tximport)) (native-inputs (list r-knitr)) @@ -24604,13 +25057,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "06gnpjcniqm8i52xh9xl3nn0wm9nn9rkqd3w3fjv7ii142xypjln")))) + (base32 "0a8q4wcqcxs7933bxg9bg03ps6hnybvcpqmlpz1pjy3affzghcbi")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs |