diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 484 |
1 files changed, 334 insertions, 150 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7ff364ee55..a7af5c42ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net> ;;; 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> @@ -2887,13 +2887,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "1gydc2sy0lf2h83dzr60w9k3ipqd8h62q6764xpn31girwx70rdz")))) + "0cimi60asz5mmrq2qmnyqq9x5yg14cc67j8135x9zlklblsfyf35")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs @@ -3300,13 +3300,13 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "0syd1m992i2xqw2djw6s07zwwvrzvd0aksix1cbhx9plpswd2245")))) + "06n0as71m3dfbnzjfq8f1s0r40w4flc8am7zb0293c1037clmcig")))) (properties `((upstream-name . "AnVIL"))) (build-system r-build-system) (propagated-inputs @@ -3862,13 +3862,13 @@ pairs.") (define-public r-aseb (package (name "r-aseb") - (version "1.46.0") + (version "1.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1hiapxdbp1fg6wk62s31nkv9mkxzvd23hn3zhmf9n0nvqfhi7bdf")))) + "1da6ld3ij55l3saj05ink8i1f6gqwyrv896qh8g94dmh6vzn2xbr")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") @@ -4408,13 +4408,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "1xdyi61scfay5l5v7c40wjjl83kcvagvypxnfvsws4avh08x3ni3")))) + "0y81m37c5irpaw9pfm5b672wk804n4x1g9g5pfh1dp7pggfwbf1z")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -4516,14 +4516,14 @@ retrieval analyses, or similar technologies.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.18.0") + (version "3.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "07zcf19gcbki2d18xgyrdzp3vn90cz2ww45p8ra4lc1mif5gy0c3")))) + "15wr651ylbx3am213dsy5kdr1xc8r5c9rfq5ydxzqlmxzjgymj55")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -4628,13 +4628,13 @@ stochastic dropout events as well as systematic allelic imbalance is used.") (define-public r-cellid (package (name "r-cellid") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CelliD" version)) (sha256 (base32 - "1x4kp8i204rqas2bgg4qanwdncafilymlpvxvfyv39zpdji91yv5")))) + "13hwxhdp268h3n8d8wgr75i60apa9mama9bg049yz7c6mj5ixd1v")))) (properties `((upstream-name . "CelliD"))) (build-system r-build-system) (propagated-inputs @@ -5269,13 +5269,13 @@ bases such as COSMIC.") (define-public r-degreport (package (name "r-degreport") - (version "1.38.0") + (version "1.38.5") (source (origin (method url-fetch) (uri (bioconductor-uri "DEGreport" version)) (sha256 (base32 - "1ska9fh1bzdqd9pi67vqgx0vz4wz2r5kzmh73fb9zh9m0gnjjr23")) + "0s0d40ac1da73w7j96lb20wchgs4c2svfrafsgi9mx5hiswfz25z")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "DEGreport"))) @@ -5298,6 +5298,7 @@ bases such as COSMIC.") r-complexheatmap r-consensusclusterplus r-cowplot + r-dendextend r-deseq2 r-dplyr r-edger @@ -5313,6 +5314,7 @@ bases such as COSMIC.") r-rlang r-s4vectors r-scales + r-stringi r-stringr r-summarizedexperiment r-tibble @@ -5481,19 +5483,18 @@ calculation in parallel.") (define-public r-dmrcate (package (name "r-dmrcate") - (version "2.14.1") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DMRcate" version)) (sha256 (base32 - "1va60r297cl6xw5mc4nf9igfizqqzz7i5436x26iw4q35jcwlfjl")))) + "19dxpmjjg8v2l71yjjlfj0ycvmhi9rk04q59nwjcp0aw8nvk6l3w")))) (properties `((upstream-name . "DMRcate"))) (build-system r-build-system) (propagated-inputs (list r-biomart r-bsseq - r-dss r-edger r-experimenthub r-genomeinfodb @@ -5700,14 +5701,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "1yxg04644yqy3wbqbsf4hcvvimkk8z60xizpy4rc48i3hxjm7nbf")))) + "1d9in3hs2n91pv498715d3qi82c7xsnm42vnzgfyz096zjghgp7a")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -6197,14 +6198,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1h065fhw0n2ga74csyhqbj4qfhkg058pqa684ixcski4rhsd7hcf")))) + "0bgv8a7hf8ns472zfryf255zqdikjv08np6k6hkpvyivad25vpwy")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -6215,8 +6216,8 @@ problems in CEL-level data to help evaluate performance of quality metrics.") r-dbi r-edger r-gcrma - r-glimma r-ggplot2 + r-glimma r-gostats r-gplots r-hwriter @@ -6318,13 +6319,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.64.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0nyw3x5ivq969p2w788zi4pp0pwjv5hhpjpl5lyfzhak9ydylgh6")))) + "1bdr303a2z03c8vc8q95a4a4a8i956vimia5yik78yddd1ig9gq3")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6563,13 +6564,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biomartr (package (name "r-biomartr") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "biomartr" version)) (sha256 (base32 - "06wd8s2cssw58xp9d078fc7iycpxryccnclrk3gnh757j1h0vzim")))) + "0ic6qbk2xmgrcc0xhxyhjafp1xbf2c5dpbqqrbkprrhynr8mq7cx")))) (properties `((upstream-name . "biomartr"))) (build-system r-build-system) (propagated-inputs @@ -6793,13 +6794,13 @@ analysis.") (define-public r-champ (package (name "r-champ") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChAMP" version)) (sha256 (base32 - "1px2pm90lxwh0yn7h1kmmf94flhjs5p4i0iav7ya1xfybyg4w2zc")))) + "1gdcdx34bxffd6ch354qx7yjngx3lj9chv5frwjyk56jq12vjjk7")))) (properties `((upstream-name . "ChAMP"))) (build-system r-build-system) (propagated-inputs @@ -7323,13 +7324,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.0.1") + (version "4.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0vjydwjazl7br0hvshy7jip3z6w73bif9vaky20im5rv40pqnchh")))) + "16cghh83v14jdq5n6xkm3jxj87n6l6zrxjgqdwb2ffgc26vkpb7w")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7461,6 +7462,37 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) +(define-public r-epidish + (package + (name "r-epidish") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EpiDISH" version)) + (sha256 + (base32 "170ym3y6gd1kxghz2g5ynvgi1wrxx87b568cjcvzidpqkrkg87s6")))) + (properties `((upstream-name . "EpiDISH"))) + (build-system r-build-system) + (propagated-inputs (list r-e1071 + r-locfdr + r-mass + r-matrix + r-matrixstats + r-quadprog + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/sjczheng/EpiDISH") + (synopsis "Epigenetic dissection of intra-sample-heterogeneity") + (description + "@code{EpiDISH} is a R package to infer the proportions of a priori known +cell-types present in a sample representing a mixture of such cell-types. +Right now, the package can be used on DNAm data of whole blood, generic +epithelial tissue and breast tissue. Besides, the package provides a function +that allows the identification of differentially methylated cell-types and +their directionality of change in Epigenome-Wide Association Studies.") + (license license:gpl2))) + (define-public r-fastseg (package (name "r-fastseg") @@ -7610,13 +7642,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.38.0") + (version "1.38.5") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1a82xx1ijmfxk6d4pjqy45cdrnf75yrs7l7l64brl5d5dif45s42")))) + "17w5zrvpk2x0sc55xfkbn9krphg4aszmvwmj1qfsf1bdrazfpwic")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -8288,7 +8320,6 @@ methylation data at the genome scale.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) -;; TODO: check javascript (define-public r-interactivedisplay (package (name "r-interactivedisplay") @@ -8301,40 +8332,50 @@ microarray data, using nearest neighbor averaging.") "0w81c5kc48gjavln50ysgr3vaf8s4fb6632ckzb1q225j9ik2gia")) (snippet '(for-each delete-file - '("inst/www/js/jquery.js" + '("inst/www/js/d3.v2.js" + "inst/www/js/jquery.js" "inst/www/js/jquery.min.js" - "inst/www/js/jquery.dataTables.min.js"))))) + "inst/www/js/jquery.dataTables.min.js" + "inst/www/js/jquery.dataTables.nightly.js"))))) (properties `((upstream-name . "interactiveDisplay"))) (build-system r-build-system) (arguments (list - #:modules '((guix build utils) - (guix build r-build-system) - (srfi srfi-1)) + #:modules + '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'process-javascript - (lambda* (#:key inputs #:allow-other-keys) - (call-with-values - (lambda () - (unzip2 - `((,(assoc-ref inputs "js-jquery-1.8.2") - "inst/www/js/jquery.js") - (,(assoc-ref inputs "js-jquery-1.9.1") - "inst/www/js/jquery.min.js") - (,(search-input-file inputs - "/share/javascript/jquery.dataTables.min.js") - "inst/www/js/jquery.dataTables.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - sources targets)))))))) + #~(modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/" + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(assoc-ref inputs "js-jquery-1.8.2") + . "www/js/jquery.js") + (,(assoc-ref inputs "js-jquery-1.9.1") + . "www/js/jquery.min.js") + (,(search-input-file inputs + "/share/javascript/jquery.dataTables.min.js") + . "www/js/jquery.dataTables.min.js") + (,(string-append (assoc-ref inputs "js-datatables-1.9") + "/share/javascript/jquery.dataTables.min.js") + . "www/js/jquery.dataTables.min.js") + (,(string-append (assoc-ref inputs "js-datatables-1.10") + "/share/javascript/jquery.dataTables.min.js") + . "www/js/jquery.dataTables.nightly.js") + (,(assoc-ref inputs "js-d3-v2") + . "www/js/d3.v2.js"))))))))) (propagated-inputs (list r-annotationdbi r-biocgenerics + r-biocmanager ;this is not listed in DESCRIPTION r-category r-ggplot2 r-gridsvg @@ -8347,7 +8388,15 @@ microarray data, using nearest neighbor averaging.") (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) - ("js-datatables" ,js-datatables) + ("js-d3-v2" + ,(origin + (method url-fetch) + (uri "https://web.archive.org/web/20230428092426id_/https://d3js.org/d3.v2.js") + (sha256 + (base32 + "1m57mxhcynfaz6gz3v0aph5i6hx5jf455jdygyl8yzs9r2dpp5vr")))) + ("js-datatables-1.9" ,js-datatables-1.9) + ("js-datatables-1.10" ,js-datatables) ("js-jquery-1.8.2" ,(origin (method url-fetch) @@ -9102,14 +9151,14 @@ package TeXshade.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.28.0") + (version "2.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0dway94j3k2dq5p8lqzj49ql85xrxxxgmlgppqg0h8k56xqrmf5i")))) + "1622mmm5n8yl4qjq8bda7689qdfz1rhyxyh8s3q5475al1d0mpsl")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9592,6 +9641,34 @@ package contains functions for combining the results of multiple runs of gene set analyses.") (license license:gpl2+))) +(define-public r-polyester + (package + (name "r-polyester") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "polyester" version)) + (sha256 + (base32 "1iycdxj0jhh2faclfzflp2cjc2zmxmhy03avv75h0qg3j5kf35l4")))) + (properties `((upstream-name . "polyester"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-iranges + r-limma + r-logspline + r-s4vectors + r-zlibbioc)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/polyester") + (synopsis "Simulate RNA-seq reads") + (description + "The polyester package simulates RNA-seq reads from differential expression +experiments with replicates. The reads can then be aligned and used to perform +comparisons of methods for differential expression.") + (license license:artistic2.0))) + (define-public r-powertcr (package (name "r-powertcr") @@ -9792,18 +9869,16 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.39.0") + (version "2.42.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "15h7vqdxfv7y0f82ff7a8brqnscs324x22izlkgjk2wqahnmr2l1")) + "109vmrdsjdjnfrlcdyadzbwz9a50hqaahf7dawwxkbbh4mmdih78")) (snippet - '(for-each delete-file - (list "inst/doc/jslib/jquery-1.8.0.min.js" - "inst/extdata/jslib/jquery-1.8.0.min.js"))))) + '(delete-file "inst/extdata/jslib/jquery-1.8.0.min.js")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -9811,25 +9886,20 @@ region sets and other genomic features.") (list #:modules '((guix build utils) (guix build r-build-system) - (srfi srfi-1)) + (guix build minify-build-system) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) #:phases - '(modify-phases %standard-phases + '(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) - (call-with-values - (lambda () - (unzip2 - `((,(assoc-ref inputs "_") - "inst/doc/jslib/jquery-1.8.0.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - sources targets))) - (copy-file "inst/doc/jslib/jquery-1.8.0.min.js" - "inst/extdata/jslib/jquery-1.8.0.min.js")))))) + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(assoc-ref inputs "_") + . "inst/extdata/jslib/jquery-1.8.0.min.js")))))))) (propagated-inputs (list r-annotate r-annotationdbi @@ -9851,7 +9921,7 @@ region sets and other genomic features.") r-r-utils r-xml)) (native-inputs - (list esbuild r-knitr + (list esbuild r-rmarkdown (origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.8.0.js") @@ -9875,13 +9945,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.46.0") + (version "2.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1csf5nrg2nkdwh8cz26idz6wrhj7bgnfh559mzlpdj4licnf1ymc")))) + "0yfy0y9ywzbbdmvvraxmizv3w2x1iznhfys6hhwyi644pxh4k3xn")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib r-s4vectors)) @@ -9902,14 +9972,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "1appjnggyljrn77nvv9adkwxplbrrlgkrrd1bf2b5r0nsa505hdc")))) + "0cqf7k19k4m4swd2c1wd9cyzw9k90s3d3jq0hijjwvza50nn2dk6")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (arguments @@ -10276,6 +10346,49 @@ comprehensive scDblFinder method.") (license license:gpl3))) ;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-scgate + (package + (name "r-scgate") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scGate" version)) + (sha256 + (base32 "0h12d36zjc6fvxbhkxrzbpvw49z9fgyn1jc941q70ajw1yqi2hhh")))) + (properties `((upstream-name . "scGate"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-dplyr + r-ggplot2 + r-ggridges + r-patchwork + r-reshape2 + r-seurat + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/carmonalab/scGate") + (synopsis + "Marker-based cell type purification for single-cell sequencing data") + (description + "This package provides a method to purify a cell type or cell population +of interest from heterogeneous datasets. scGate package automatizes +marker-based purification of specific cell populations, without requiring +training data or reference gene expression profiles. scGate takes as input a +gene expression matrix stored in a Seurat object and a @acronym{GM, gating +model}, consisting of a set of marker genes that define the cell population of +interest. It evaluates the strength of signature marker expression in each +cell using the rank-based method UCell, and then performs @acronym{kNN, +k-nearest neighbor} smoothing by calculating the mean UCell score across +neighboring cells. kNN-smoothing aims at compensating for the large degree of +sparsity in scRNAseq data. Finally, a universal threshold over kNN-smoothed +signature scores is applied in binary decision trees generated from the +user-provided gating model, to annotate cells as either “pure” or “impure”, +with respect to the cell population of interest.") + (license license:gpl3))) + +;; This is a CRAN package, but it depends on packages from Bioconductor. (define-public r-scistreer (package (name "r-scistreer") @@ -10397,6 +10510,38 @@ expression information. The package functions as a wrapper for Startrac and powerTCR R packages.") (license license:gpl2))) +(define-public r-scrnaseq + (package + (name "r-scrnaseq") + (version "2.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scRNAseq" version + 'experiment)) + (sha256 + (base32 "0dbh3sqq7lkkdf7vls5qg7fbn6y74c7hsigb4d69pvk934ll88aw")))) + (properties `((upstream-name . "scRNAseq"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-annotationhub + r-biocgenerics + r-ensembldb + r-experimenthub + r-genomicfeatures + r-genomicranges + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scRNAseq") + (synopsis "Collection of public single-cell RNA-seq datasets") + (description + "This package contains gene-level counts for a collection of public +@code{scRNA-seq} datasets, provided as @code{SingleCellExperiment} objects +with cell- and gene-level metadata.") + (license license:cc0))) + (define-public r-scry (package (name "r-scry") @@ -10699,13 +10844,13 @@ level.") (define-public r-tcgautils (package (name "r-tcgautils") - (version "1.22.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAutils" version)) (sha256 (base32 - "0r79iiqv7q83wz5w3lm271dn3jdrkggmvjdyj1wnjsih1n2viy7d")))) + "16pcz52ynx0syb5bcnkywllqxcfp7jipqgzgjr7q70k1z13ah7a3")))) (properties `((upstream-name . "TCGAutils"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -10754,17 +10899,55 @@ identifier translation via the GDC API.") "This package implements widgets to provide user interfaces.") (license license:artistic2.0))) +(define-public r-toast + (package + (name "r-toast") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TOAST" version)) + (sha256 + (base32 "00wpgs2zdrgrh9xmp6m5h9xgv85mhdi36qvwg9gwbz9i7cfabmy1")))) + (properties `((upstream-name . "TOAST"))) + (build-system r-build-system) + (propagated-inputs (list r-corpcor + r-doparallel + r-epidish + r-ggally + r-ggplot2 + r-limma + r-nnls + r-quadprog + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TOAST") + (synopsis "Tools for the analysis of heterogeneous tissues") + (description + "This package is devoted to analyzing high-throughput data (e.g. gene +expression microarray, DNA methylation microarray, RNA-seq) from complex +tissues. Current functionalities include + +@enumerate +@item detect cell-type specific or cross-cell type differential signals +@item tree-based differential analysis +@item improve variable selection in reference-free deconvolution +@item partial reference-free deconvolution with prior knowledge. +@end enumerate") + (license license:gpl2))) + ;; TODO: check javascript (define-public r-trackviewer (package (name "r-trackviewer") - (version "1.38.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "trackViewer" version)) (sha256 (base32 - "15agkyqx6gl5zzdxra5nl0czd4j7mw456r587w039l9hzwznwbr8")) + "008d1wg8882iq7jfmwijpchxrfva5ysl45ama62iy8s9dm0fpwsj")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "trackViewer"))) @@ -11354,13 +11537,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.48.0") + (version "1.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1r1cyimr5l5jzgxvmrm3vq8mvz3f1klfdwy9mz31xvnvgjacr58p")))) + "0l9xkrvsrc3m65kdjcyir6jkpa718g7idziwr0pp5yaj84bd3xia")))) (properties `((upstream-name . "VariantAnnotation"))) (build-system r-build-system) @@ -11578,13 +11761,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "02q9icblcnh0l7vah29mnhcczw8w0gpgd57v19gy7222nrqpcd9m")))) + (base32 "029bqn25c90algvgacxbv0fdznpg879xjwfj5hiydfwq30y0kr8r")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -13046,14 +13229,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas")))) + "0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -13203,14 +13386,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "1nhxwj6gwc3hqji7icp1q6n0hj1gnvv1y5zhd2myhm7kj3sic2qc")))) + "05cy3xvj78n2p9l2pxfys7aczr51gm2ywprn4qmzr7ppb6rq5f66")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -13689,14 +13872,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1d5zik3bhz26ky2kpxd9kdzs9ff696qqys5gl8qwmmp8qym520l2")))) + "1z4ddkdd3mzqg0c6l94qmrdwrm7427k5xiwzgkzx43gh1j4911d5")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -14561,13 +14744,13 @@ and Infinium HD arrays are also included.") (define-public r-lefser (package (name "r-lefser") - (version "1.11.5") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lefser" version)) (sha256 (base32 - "1fnccnjllgxf51dlmcvv0r66xs0wvfxrj66qrqisqd99hrpxhws2")))) + "0aywwinp4wwwa12rq60gpfk5gn28zyimayxakgj4lhfwjk0byz8m")))) (properties `((upstream-name . "lefser"))) (build-system r-build-system) (propagated-inputs @@ -15074,14 +15257,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.28.0") + (version "3.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1xirazskw2d0fllyf27jvsm69amcil1znx81m9d613vl03dpwswy")))) + "0kk4l8cxyvcq4cjjnb59zajf4ci0igml13582qqn8123cqkbf8pf")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -15091,10 +15274,9 @@ to multiple hypothesis correction.") r-ggplot2 r-gosemsim r-hdo-db - r-hpo-db - r-mpo-db r-qvalue - r-reshape2)) + r-reshape2 + r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/DOSE/") @@ -15783,14 +15965,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.14.1") + (version "2.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1plpmi1sb9vv03480njf3awnc7i19f9iaxi3j6bvjzpi6zmw40dq")))) + "0rhyfbm5whz4jygar9cqcrfy92h1lyam5wd8d9svhh80f15v53m9")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -16512,14 +16694,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "4.0.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "10bvxww489mb4bl5v9ma6klyg359zb9ady5rl95q1mkp54hahdw8")))) + "061ihzj8pn2g393q1gdq2jssanxm9gh5qm37fz4gna2hbd6bf79p")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -17719,14 +17901,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.14.0") + (version "4.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "09cpbf33b3x9b06yf41qy2fy8zviwrznrpkb9fq3an8vg8gf51lp")))) + "0sbixbq99kmhh0ppdid1hqhb75yxb6gsm5pdz75y67i3pgwrv1sj")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -18700,14 +18882,14 @@ populations, splice site strength, conservation, etc.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.32.1") + (version "1.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1pr321hv5q2sl8lc998hkwdl2mfyzcgf2l70ny2m3hfmlclq5lnn")))) + "0cmcg39a5939y517vhvwanqh1fwzyx6pbq47nc5cpswf7pn9cv5x")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -18725,6 +18907,7 @@ populations, splice site strength, conservation, etc.") r-lmertest r-mass r-matrix + r-matrixstats r-pbkrtest r-rdpack r-remacor @@ -18778,13 +18961,13 @@ features (e.g. genes, microRNAs).") (define-public r-ucell (package (name "r-ucell") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "UCell" version)) (sha256 (base32 - "1ds11f1q6v89sfcj1sinrkv7aw3s0prf5nxf7pz4hdsvqn4zp467")))) + "00v4b91f7y3zyndbl4wlfay8wljnqypfc05vrw15yr62d9smd35d")))) (properties `((upstream-name . "UCell"))) (build-system r-build-system) (propagated-inputs (list r-biocneighbors @@ -20367,14 +20550,14 @@ plot them, and perform logrank or Wilcoxon type tests.") (define-public r-fhtest (package (name "r-fhtest") - (version "1.5") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "FHtest" version)) (sha256 (base32 - "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q")))) + "0x7lr88w0b09ng7nps490kgj8aqdjzmp9skv9iwqgn871pnpydms")))) (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs @@ -20499,13 +20682,13 @@ array-like semantic. It also provides: (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.40.1") + (version "0.40.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0pja00ssl1pd16v3bls3aybml2cwanylx8igf596zha5srcf5l5h")))) + "10lryil0psfyal0006rbhj0dbxyn8f7mpp11h758zc217cxsdnac")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -20529,14 +20712,14 @@ S4Vectors package itself.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.72-1") + (version "1.72-5") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1p3zsl5r6l5r6ylnrxmbxjpim5qgmncgdjcgn5j69rzk3rv85gqx")))) + "17g7lan1rpy6y4nmqksrf9ddp3gs58vdczfavgq1fp13zx1r2hq3")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -20548,10 +20731,10 @@ S4Vectors package itself.") r-go-db r-hmisc r-impute - r-rcpp - r-survival r-matrixstats - r-preprocesscore)) + r-preprocesscore + r-rcpp + r-survival)) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") @@ -20726,14 +20909,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "10n2grfdnri686sx52shz7y0csmcz4cky23k07803dz6qm1ljvmf")) + "0lb5dkzfnfvxwrk8s9vzfjp8ab1sbr7b22jnzg41hgmpysi7dswh")) (modules '((guix build utils))) (snippet '(begin @@ -20794,10 +20977,11 @@ block processing.") (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - (list hdf5-1.10 zlib)) + (list hdf5-1.10 r-biocstyle r-stringr zlib)) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) - ("r-knitr" ,r-knitr))) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R @@ -21205,13 +21389,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0a8wfrcp09z0aflalqhhwvz675aa32wgprqphk1axvdppknsg7vf")))) + "06a4nxxsgmi435m06ir401w4fbrh0xdgh6mkv3i7vw001yrbrfcx")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -21292,13 +21476,13 @@ variable and significantly correlated genes.") (define-public r-sparsearray (package (name "r-sparsearray") - (version "1.2.0") + (version "1.2.3") (source (origin (method url-fetch) (uri (bioconductor-uri "SparseArray" version)) (sha256 - (base32 "0a1xg8vkjybgdr09bk2z4i82m06qnw2nhbzviyijadxiwvz6pgsz")))) + (base32 "19cy1nmmi65fxh012ymgp1kg112yl1m0khcs4y034p5iwlfv7fp6")))) (properties `((upstream-name . "SparseArray"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -21420,14 +21604,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "0faj4fxfsv7ir935sn9zainhk55vdfi6abgr0s321kwmvs6prc0p")))) + "0l6rdkpg89pds3n5y4khvaifgbvm38n0vlpi15h97rnk8x461rsz")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -21834,14 +22018,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.46.0") + (version "1.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0b707xxi0ch4kfxid5id16gkh9pnqwrgqpsvgbm0rc89kg73g4jz")))) + "0an8hd2g2hp3p1vfsmxq77fm71xlf5g73j4w5mcy28x1aj073zxf")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -22029,14 +22213,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "3.0.3") + (version "3.0.4") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "1yh9nhfphalxh77132r0fkpp71mqsfhb8jk11is4d5nvlvr5316z")))) + "1qqsm6ldbf6rnzvspcnv87l4mkxccg4divzf6nj7j92jnhyadqia")))) (build-system r-build-system) (inputs (list gsl)) @@ -22710,14 +22894,14 @@ input.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "08wsn2znw56svyv5vpxxzcynz93h5hzw1n2r6hb9h3rvc7afyvxl")))) + "19m4h90rkk6mizllkih2xmxag8nb45qss3vydkkyj62s5zjhfh27")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -22734,14 +22918,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1z482gw04psvkgspclmxlkd9qi7srgbnr56ajngcng28sc6zqdhs")))) + "1v67z53y2nnss6l6nk7f557kn0d5syg9n0zdgddpsz26rwdmp8ai")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -23101,14 +23285,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.38.0") + (version "1.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn")))) + "1imni8lpjzf53w2q34ql0j9rwq6drbzxvs0nhzf6s172iqym2hq3")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (arguments @@ -23724,14 +23908,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0wn7r1dzckiq3zacvcv2w780fj9bvz1vbyzcazv2qvsicbwc4vd8")))) + "00wygiv6k75bx5qs27qlq9l6ajv9gl2bbyqi2gv6jaaaj167q4sd")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |