diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 2946 |
1 files changed, 1927 insertions, 1019 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55d397e5cf..176f7ecc6d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> -;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> @@ -358,14 +358,14 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") (define-public r-bsgenome-hsapiens-ucsc-hg19-masked (package (name "r-bsgenome-hsapiens-ucsc-hg19-masked") - (version "1.3.99") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" - version 'annotation)) - (sha256 - (base32 - "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) + (version "1.3.993") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" + version 'annotation)) + (sha256 + (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) (build-system r-build-system) @@ -557,6 +557,32 @@ several related annotation packages.") from several related annotation packages.") (license license:artistic2.0))) +(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 + (package + (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri + "IlluminaHumanMethylation450kanno.ilmn12.hg19" + version 'annotation)) + (sha256 + (base32 + "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) + (properties + `((upstream-name + . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (home-page + "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") + (synopsis "Annotation for Illumina's 450k methylation arrays") + (description + "This package provides manifests and annotation for Illumina's 450k array +data.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -670,14 +696,14 @@ annotations for the genome of the model mouse Mus musculus.") (define-public r-bsgenome-hsapiens-ucsc-hg19 (package (name "r-bsgenome-hsapiens-ucsc-hg19") - (version "1.4.0") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" version 'annotation)) (sha256 (base32 - "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) + "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) @@ -694,14 +720,13 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") (define-public r-bsgenome-hsapiens-ucsc-hg38 (package (name "r-bsgenome-hsapiens-ucsc-hg38") - (version "1.4.1") + (version "1.4.4") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" version 'annotation)) (sha256 - (base32 - "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) + (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) @@ -775,6 +800,44 @@ Ensembl.") Ensembl.") (license license:artistic2.0))) +(define-public r-snplocs-hsapiens-dbsnp144-grch37 + (package + (name "r-snplocs-hsapiens-dbsnp144-grch37") + (version "0.99.20") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" + version 'annotation)) + (sha256 + (base32 + "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) + (build-system r-build-system) + ;; As this package provides little more than a very large data file it + ;; doesn't make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (propagated-inputs + (list r-biocgenerics + r-s4vectors + r-iranges + r-genomeinfodb + r-genomicranges + r-bsgenome + r-biostrings)) + (home-page + "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") + (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") + (description "This package provides SNP locations and alleles for Homo +sapiens extracted from NCBI dbSNP Build 144. The source data files used for +this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped +to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a +patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, +X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for +the mitochondrion chromosome. Therefore, the SNPs in this package can be +injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the +correct position but this injection will exclude chrM (i.e. nothing will be +injected in that sequence).") + (license license:artistic2.0))) + (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene (package (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene") @@ -828,19 +891,18 @@ track. The database is exposed as a @code{TxDb} object.") (define-public r-txdb-hsapiens-ucsc-hg38-knowngene (package (name "r-txdb-hsapiens-ucsc-hg38-knowngene") - (version "3.4.6") + (version "3.15.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" version 'annotation)) (sha256 - (base32 - "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) + (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs - (list r-genomicfeatures)) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -1017,14 +1079,13 @@ data (chip hgu133plus2) assembled using data from public repositories.") (define-public r-pfam-db (package (name "r-pfam-db") - (version "3.8.2") + (version "3.15.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PFAM.db" version 'annotation)) (sha256 - (base32 - "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) + (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7")))) (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs @@ -1102,74 +1163,52 @@ datasets which are derived from the Allen Brain Atlas: All datasets are restricted to protein coding genes.") (license license:gpl2+))) +(define-public r-adductdata + (package + (name "r-adductdata") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "adductData" version 'experiment)) + (sha256 + (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48")))) + (properties `((upstream-name . "adductData"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationhub r-experimenthub)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/adductData") + (synopsis "Data from untargeted mass spectrometry of modifications to Cys34") + (description + "This package contains data from untargeted @dfn{mass spectrometry} (MS) +of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum +albumin} (HSA).") + (license license:artistic2.0))) + (define-public r-aneufinderdata (package (name "r-aneufinderdata") - (version "1.18.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinderData" version 'experiment)) (sha256 - (base32 - "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks")))) + (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/AneuFinderData/") (synopsis "Data package for @code{AneuFinder}") - (description "This package contains data used by @code{AneuFinder}.") + (description "This package contains whole-genome single cell sequencing data for +demonstration purposes in the @code{AneuFinder} package.") (license license:artistic2.0))) -(define-public r-aneufinder - (package - (name "r-aneufinder") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AneuFinder" version)) - (sha256 - (base32 - "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) - (build-system r-build-system) - (native-inputs - (list r-knitr)) - (propagated-inputs - (list r-genomicranges - r-aneufinderdata - r-ecp - r-foreach - r-doparallel - r-biocgenerics - r-s4vectors - r-genomeinfodb - r-iranges - r-rsamtools - r-bamsignals - r-dnacopy - r-biostrings - r-genomicalignments - r-ggplot2 - r-reshape2 - r-ggdendro - r-ggrepel - r-reordercluster - r-mclust - r-cowplot)) - (home-page "https://bioconductor.org/packages/AneuFinder/") - (synopsis "Copy number variation analysis in single-cell-sequencing data") - (description "This package implements functions for copy number variant -calling, plotting, export and analysis from whole-genome single cell -sequencing data.") - (license license:artistic2.0))) - (define-public r-arrmdata (package (name "r-arrmdata") - (version "1.18.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmData" version 'experiment)) (sha256 - (base32 - "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) + (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p")))) (properties `((upstream-name . "ARRmData"))) (build-system r-build-system) @@ -1183,14 +1222,13 @@ from Illumina 450k methylation arrays.") (define-public r-biscuiteerdata (package (name "r-biscuiteerdata") - (version "1.6.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteerData" version 'experiment)) (sha256 - (base32 - "1d7zibjf0qccmdnzdxh7wy1h943yhnbf8zdix72486pvhzm124zj")))) + (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw")))) (properties `((upstream-name . "biscuiteerData"))) (build-system r-build-system) @@ -1207,13 +1245,13 @@ biscuiteer.") (define-public r-celldex (package (name "r-celldex") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "celldex" version 'experiment)) (sha256 - (base32 "04w60fx3s3wlirmr65nsz6d7ig48j9fzimdr8kbdqv1g80ivdcq1")))) + (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10")))) (properties `((upstream-name . "celldex"))) (build-system r-build-system) (propagated-inputs @@ -1236,14 +1274,13 @@ single-cell data or deconvolution of bulk RNA-seq.") (define-public r-chromstardata (package (name "r-chromstardata") - (version "1.16.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaRData" version 'experiment)) (sha256 - (base32 - "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab")))) + (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1")))) (properties `((upstream-name . "chromstaRData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/chromstaRData/") @@ -1253,45 +1290,16 @@ single-cell data or deconvolution of bulk RNA-seq.") chromstaR package.") (license license:gpl3))) -(define-public r-chromvarmotifs - (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") - (revision "1")) - (package - (name "r-chromvarmotifs") - (version (git-version "0.2.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/GreenleafLab/chromVARmotifs") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) - (properties `((upstream-name . "chromVARmotifs"))) - (build-system r-build-system) - (propagated-inputs - `(("r-tfbstools" ,r-tfbstools))) - (home-page "https://github.com/GreenleafLab/chromVARmotifs") - (synopsis "Stores motif collections for use with motifmatchr or chromVAR") - (description - "This package stores motif collections as lists of @dfn{position -frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools} -package for use in R with packages like @code{motifmatchr} or -@code{chromVAR}.") - (license license:expat)))) - (define-public r-copyhelper (package (name "r-copyhelper") - (version "1.6.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) (sha256 - (base32 - "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1")))) (properties `((upstream-name . "CopyhelpeR"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/CopyhelpeR/") @@ -1308,14 +1316,13 @@ GenomicRanges Bioconductor package.") (define-public r-genelendatabase (package (name "r-genelendatabase") - (version "1.18.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) (sha256 - (base32 - "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) + (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz")))) (properties `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) @@ -1331,13 +1338,13 @@ genomes and gene ID formats, largely based on the UCSC table browser.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "genomationData" version 'experiment)) - (sha256 - (base32 - "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "genomationData" version 'experiment)) + (sha256 + (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh")))) (properties `((upstream-name . "genomationData"))) (build-system r-build-system) @@ -1354,19 +1361,42 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-msdata + (package + (name "r-msdata") + (version "0.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "msdata" version 'experiment)) + (sha256 + (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691")))) + (properties `((upstream-name . "msdata"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/msdata") + (synopsis "Various Mass Spectrometry raw data example files") + (description + "This package provides Ion Trap positive ionization mode data in mzML file +format. It includes a subset from 500-850 m/z and 1190-1310 seconds, +including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex +III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5; +LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example +files for various search engines.") + (license license:gpl2+))) + (define-public r-pasilla (package (name "r-pasilla") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "pasilla" version 'experiment)) - (sha256 - (base32 - "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pasilla" version 'experiment)) + (sha256 + (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib")))) (build-system r-build-system) - (propagated-inputs - (list r-biocstyle r-dexseq r-knitr r-rmarkdown)) + (propagated-inputs (list r-dexseq)) + (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts @@ -1378,13 +1408,13 @@ by Brooks et al., Genome Research 2011.") (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") - (version "1.2.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) - (sha256 - (base32 - "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) + (sha256 + (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v")))) (properties `((upstream-name . "HSMMSingleCell"))) (build-system r-build-system) @@ -1407,13 +1437,13 @@ resulting in a complete gene expression profile for each cell.") (define-public r-all (package (name "r-all") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "ALL" version 'experiment)) - (sha256 - (base32 - "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ALL" version 'experiment)) + (sha256 + (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs @@ -1431,14 +1461,13 @@ the form of an @code{exprSet} object.") (define-public r-affydata (package (name "r-affydata") - (version "1.32.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affydata" version 'experiment)) (sha256 - (base32 - "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) + (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp")))) (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs @@ -1454,13 +1483,13 @@ package @code{affy}.") (define-public r-gagedata (package (name "r-gagedata") - (version "2.28.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gageData" version 'experiment)) (sha256 - (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn")))) + (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9")))) (properties `((upstream-name . "gageData"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/gageData") @@ -1480,14 +1509,13 @@ yeast are also included.") (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") - (version "1.8.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 - (base32 - "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) + (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr")))) (properties `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) @@ -1498,6 +1526,7 @@ yeast are also included.") r-multiassayexperiment r-s4vectors r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description @@ -1513,13 +1542,13 @@ across the entire multi-'omics experiment.") (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment)) (sha256 - (base32 "08zmlvycq3jz1zy0715x9f21nf3465c51k7w2jq12sfbap36pmjm")))) + (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g")))) (properties `((upstream-name . "TCGAbiolinksGUI.data"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1532,17 +1561,485 @@ TCGAbiolinksGUI package.") ;;; Packages +(define-public r-abarray + (package + (name "r-abarray") + (version "1.64.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ABarray" version)) + (sha256 + (base32 + "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r")))) + (properties `((upstream-name . "ABarray"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-multtest)) + (home-page "https://bioconductor.org/packages/ABarray") + (synopsis + "Gene expression analysis for Applied Biosystems Genome Survey Microarray") + (description + "The package @code{ABarray} is designed to work with Applied Biosystems +whole genome microarray platform, as well as any other platform whose data can +be transformed into expression data matrix. Functions include data +preprocessing, filtering, control probe analysis, statistical analysis in one +single function. A @dfn{graphical user interface} (GUI) is also provided. The +raw data, processed data, graphics output and statistical results are organized +into folders according to the analysis settings used.") + (license license:gpl2+))) + +(define-public r-absseq + (package + (name "r-absseq") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ABSSeq" version)) + (sha256 + (base32 + "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv")))) + (properties `((upstream-name . "ABSSeq"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-locfit)) + (home-page "https://bioconductor.org/packages/ABSSeq") + (synopsis + "RNA-Seq analysis based on modelling absolute expression differences") + (description + "This package implements a new RNA-Seq analysis method and integrates two +modules: a basic model for pairwise comparison and a linear model for complex +design. RNA-Seq quantifies gene expression with reads count, which usually +consists of conditions (or treatments) and several replicates for each +condition. This software infers differential expression directly by the +counts difference between conditions. It assumes that the sum counts +difference between conditions follow a negative binomial distribution. In +addition, @code{ABSSeq} moderates the fold-changes by two steps: the +expression level and gene-specific dispersion, that might facilitate the gene +ranking by fold-change and visualization.") + (license license:gpl3+))) + +(define-public r-adam + (package + (name "r-adam") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADAM" version)) + (sha256 + (base32 + "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn")))) + (properties `((upstream-name . "ADAM"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-dt + r-go-db + r-keggrest + r-knitr + r-pbapply + r-rcpp + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADAM") + (synopsis "Gene activity and diversity analysis module") + (description + "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA) +package created to group a set of genes from comparative samples (control +versus experiment) belonging to different species according to their respective +functions. The corresponding roles are extracted from the default collections +like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG). +@code{ADAM} show their significance by calculating the p-values referring to +gene diversity and activity. Each group of genes is called @dfn{Group of +functionally associated genes} (GFAG).") + (license license:gpl2+))) + +(define-public r-adamgui + (package + (name "r-adamgui") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADAMgui" version)) + (sha256 + (base32 + "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs")))) + (properties `((upstream-name . "ADAMgui"))) + (build-system r-build-system) + (propagated-inputs + (list r-adam + r-colorramps + r-data-table + r-dplyr + r-dt + r-ggplot2 + r-ggpubr + r-ggrepel + r-ggsignif + r-go-db + r-gridextra + r-knitr + r-rcolorbrewer + r-reshape2 + r-shiny + r-shinyjs + r-stringi + r-stringr + r-testthat + r-varhandle)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADAMgui/") + (synopsis "GUI for gene activity and diversity analysis") + (description + "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI) +for the @code{ADAM} package. The @code{ADAMgui} package provides two +shiny-based applications that allows the user to study the output of the +@code{ADAM} package files through different plots. It's possible, for +example, to choose a specific @dfn{group of functionally associated +genes} (GFAG) and observe the gene expression behavior with the plots created +with the @code{GFAGtargetUi} function. Features such as differential +expression and fold change can be easily seen with aid of the plots made with +the @code{GFAGpathUi} function.") + (license license:gpl2+))) + +(define-public r-adimpute + (package + (name "r-adimpute") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADImpute" version)) + (sha256 + (base32 + "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w")))) + (properties `((upstream-name . "ADImpute"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-checkmate + r-data-table + r-drimpute + r-kernlab + r-mass + r-matrix + r-rsvd + r-s4vectors + r-saver + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADImpute") + (synopsis "Adaptive computational prediction for dropout imputations") + (description + "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically +unable to quantify the expression levels of all genes in a cell, creating a +need for the computational prediction of missing values (dropout imputation). +Most existing dropout imputation methods are limited in the sense that they +exclusively use the scRNA-seq dataset at hand and do not exploit external +gene-gene relationship information. The @code{ADImpute} package proposes two +methods to address this issue: + +@enumerate +@item a gene regulatory network-based approach using gene-gene relationships + learnt from external data; +@item a baseline approach corresponding to a sample-wide average. +@end enumerate + +@code{ADImpute} implements these novel methods and also combines them with +existing imputation methods like @code{DrImpute} and @code{SAVER}. +@code{ADImpute} can learn the best performing method per gene and combine the +results from different methods into an ensemble.") + (license license:gpl3+))) + +(define-public r-adsplit + (package + (name "r-adsplit") + (version "1.66.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "adSplit" version)) + (sha256 + (base32 + "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm")))) + (properties `((upstream-name . "adSplit"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biobase + r-cluster + r-go-db + r-keggrest + r-multtest)) + (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml") + (synopsis "Annotation-driven splits in microarray data") + (description + "This package implements clustering of microarray gene expression +profiles according to functional annotations. For each term genes are +annotated to, splits into two subclasses are computed and a significance of +the supporting gene set is determined.") + (license license:gpl2+))) + +(define-public r-affixcan + (package + (name "r-affixcan") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AffiXcan" version)) + (sha256 + (base32 + "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq")))) + (properties `((upstream-name . "AffiXcan"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-crayon + r-multiassayexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AffiXcan") + (synopsis "Functional approach to impute genetically regulated expression") + (description + "The @code{AffiXcan} package imputes a @dfn{genetically regulated +expression} (GReX) for a set of genes in a sample of individuals, using a +method based on the @dfn{total binding affinity} (TBA). Statistical models to +impute GReX can be trained with a training dataset where the real total +expression values are known.") + (license license:gpl3))) + +(define-public r-affyrnadegradation + (package + (name "r-affyrnadegradation") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AffyRNADegradation" version)) + (sha256 + (base32 + "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf")))) + (properties `((upstream-name . "AffyRNADegradation"))) + (build-system r-build-system) + (propagated-inputs (list r-affy)) + (home-page "https://bioconductor.org/packages/AffyRNADegradation") + (synopsis + "Analyze and correct probe positional bias in data due to RNA degradation") + (description + "The @code{AffyRNADegradation} package helps with the assessment and +correction of RNA degradation effects in Affymetrix 3 expression arrays. The +parameter @code{d} gives a robust and accurate measure of RNA integrity. The +correction removes the probe positional bias, and thus improves comparability +of samples that are affected by RNA degradation.") + ;; the R file header specifies GPL2 or later + (license license:gpl2+))) + +(define-public r-agdex + (package + (name "r-agdex") + (version "1.44.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AGDEX" version)) + (sha256 + (base32 + "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9")))) + (properties `((upstream-name . "AGDEX"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-gseabase)) + (home-page "https://bioconductor.org/packages/AGDEX") + (synopsis + "Evaluate agreement of differential expression for cross-species genomics") + (description + "The objective of @code{AGDEX} is to evaluate whether the results of a +pair of two-group differential expression analysis comparisons show a level of +agreement that is greater than expected if the group labels for each two-group +comparison are randomly assigned. The agreement is evaluated for the entire +transcriptome and (optionally) for a collection of pre-defined gene-sets. +Additionally, the procedure performs permutation-based differential expression +and meta analysis at both gene and gene-set levels of the data from each +experiment.") + (license license:gpl2+))) + +(define-public r-aggregatebiovar + (package + (name "r-aggregatebiovar") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "aggregateBioVar" version)) + (sha256 + (base32 + "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1")))) + (properties `((upstream-name . "aggregateBioVar"))) + (build-system r-build-system) + (propagated-inputs + (list r-matrix + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/jasonratcliff/aggregateBioVar") + (synopsis "Differential gene expression analysis for multi-subject scRNA-seq") + (description + "This package @code{aggregateBioVar} contains tools to summarize single +cell gene expression profiles at the level of subject for single cell RNA-seq +data collected from more than one subject (e.g. biological sample or technical +replicates). A @code{SingleCellExperiment} object is taken as input and +converted to a list of @code{SummarizedExperiment} objects, where each list +element corresponds to an assigned cell type. The @code{SummarizedExperiment} +objects contain aggregate gene-by-subject count matrices and inter-subject +column metadata for individual subjects that can be processed using downstream +bulk RNA-seq tools.") + (license license:gpl3))) + +(define-public r-agilp + (package + (name "r-agilp") + (version "3.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "agilp" version)) + (sha256 + (base32 + "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf")))) + (properties `((upstream-name . "agilp"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/agilp") + (synopsis "Processing of Agilent expression array") + (description + "This package aims to provide a pipeline for the low-level analysis of +gene expression microarray data, primarily focused on the Agilent platform, +but which also provides utilities which may be useful for other platforms.") + ;; Some files are under GPLv2+ but the combined work is released under the + ;; GPLv3. + (license license:gpl3))) + +(define-public r-adductomicsr + (package + (name "r-adductomicsr") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "adductomicsR" version)) + (sha256 + (base32 + "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys")))) + (properties `((upstream-name . "adductomicsR"))) + (build-system r-build-system) + (propagated-inputs + (list r-adductdata + r-ade4 + r-annotationhub + r-bootstrap + r-data-table + r-dosnow + r-dplyr + r-dt + r-experimenthub + r-fastcluster + r-foreach + r-fpc + r-mzr + r-orgmassspecr + r-pastecs + r-pracma + r-rcppeigen + r-reshape2 + r-rvest + r-smoother + r-zoo)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/adductomicsR") + (synopsis "Processing of adductomic mass spectral datasets") + (description + "This package @code{adductomicsR} processes data generated by the +@dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted +peptides from spectra that has been corrected for mass drift and retention +time drift and quantifies level mass spectral peaks from @dfn{first stage of +mass spectrometry} (MS1) data.") + (license license:artistic2.0))) + +(define-public r-agimicrorna + (package + (name "r-agimicrorna") + (version "2.46.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AgiMicroRna" version)) + (sha256 + (base32 + "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa")))) + (properties `((upstream-name . "AgiMicroRna"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-affycoretools + r-biobase + r-limma + r-preprocesscore)) + (home-page "https://git.bioconductor.org/packages/AgiMicroRna") + (synopsis + "Processing and differential expression analysis of Agilent microRNA chips") + (description + "@code{AgiMicroRna} provides useful functionality for the processing, +quality assessment and differential expression analysis of Agilent microRNA +array data. The package uses a limma-like structure to generate the processed +data in order to make statistical inferences about differential expression +using the linear model features implemented in limma. Standard Bioconductor +objects are used so that other packages could be used as well.") + (license license:gpl3))) + +(define-public r-aneufinder + (package + (name "r-aneufinder") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AneuFinder" version)) + (sha256 + (base32 + "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl")))) + (build-system r-build-system) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-genomicranges + r-aneufinderdata + r-ecp + r-foreach + r-doparallel + r-biocgenerics + r-s4vectors + r-genomeinfodb + r-iranges + r-rsamtools + r-bamsignals + r-dnacopy + r-biostrings + r-genomicalignments + r-ggplot2 + r-reshape2 + r-ggdendro + r-ggrepel + r-reordercluster + r-mclust + r-cowplot)) + (home-page "https://bioconductor.org/packages/AneuFinder/") + (synopsis "Copy number variation analysis in single-cell-sequencing data") + (description "This package implements functions for copy number variant +calling, plotting, export and analysis from whole-genome single cell +sequencing data.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") - (version "3.14.0") + (version "3.15.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik")))) + "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -1555,13 +2052,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.40.0") + (version "0.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh")))) + "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -1575,13 +2072,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) + "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors @@ -1602,13 +2099,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) + "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -1632,24 +2129,32 @@ used visualizations.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc")))) + "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 + (list r-compquadform + r-dplyr + r-ggplot2 r-kernsmooth + r-magrittr r-matrixstats r-patchwork r-pbapply + r-reshape2 + r-rlang r-statmod r-survey - r-kernsmooth)) + r-tibble + r-viridislite)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/borishejblum/dearseq") (synopsis "DEA for RNA-seq data through a robust variance component test") (description @@ -1662,13 +2167,13 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-decipher (package (name "r-decipher") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) + "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -1683,16 +2188,57 @@ set analyses, and can deal with repeated or longitudinal data.") biological sequences.") (license license:gpl3))) +(define-public r-decoupler + (package + (name "r-decoupler") + (version "2.2.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "decoupleR" version)) + (sha256 + (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m")))) + (properties `((upstream-name . "decoupleR"))) + (build-system r-build-system) + (propagated-inputs + (list r-broom + r-dplyr + r-magrittr + r-matrix + r-purrr + r-rlang + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-withr)) + (native-inputs (list r-knitr)) + (home-page "https://saezlab.github.io/decoupleR/") + (synopsis "Computational methods to infer biological activities from omics data") + (description + "Many methods allow us to extract biological activities from omics data using +information from prior knowledge resources, reducing the dimensionality for +increased statistical power and better interpretability. decoupleR is a +Bioconductor package containing different statistical methods to extract these +signatures within a unified framework. decoupleR allows the user to flexibly +test any method with any resource. It incorporates methods that take into +account the sign and weight of network interactions. decoupleR can be used +with any omic, as long as its features can be linked to a biological process +based on prior knowledge. For example, in transcriptomics gene sets regulated +by a transcription factor, or in phospho-proteomics phosphosites that are +targeted by a kinase.") + (license license:gpl3))) + (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w")))) + "0si1x2bi5pff1dicpqg7hv4ziq46vm7lic72724ljsclpz9bfv6q")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -1722,13 +2268,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.20.0") + (version "0.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj")))) + "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -1752,13 +2298,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35")))) + (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs @@ -1777,13 +2323,13 @@ calculation in parallel.") (define-public r-drimseq (package (name "r-drimseq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "0y2jb0hb633id038zmwnfny6h4ai77fdyy02f77vha1z8xg5nl02")))) + (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs @@ -1812,13 +2358,13 @@ results.") (define-public r-bluster (package (name "r-bluster") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm")))) + "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs @@ -1842,13 +2388,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) + "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -1866,13 +2412,13 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-iranges (package (name "r-iranges") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg")))) + "0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -1894,13 +2440,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf")))) + (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs @@ -2052,14 +2598,14 @@ mapping.") (define-public r-nmf (package (name "r-nmf") - (version "0.23.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) + "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs @@ -2096,14 +2642,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) + "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7")))) (build-system r-build-system) (propagated-inputs (list r-affyio @@ -2124,14 +2670,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) + "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -2145,14 +2691,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg")))) + "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -2171,14 +2717,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f")))) + "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -2194,14 +2740,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.66.0") + (version "1.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40")))) + "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -2236,14 +2782,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) + "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) @@ -2260,14 +2806,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.66.0") + (version "1.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal")))) + "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -2288,14 +2834,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) + "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -2315,13 +2861,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.56.2") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8")))) + "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -2345,13 +2891,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w")))) + "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -2370,14 +2916,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz")))) + "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -2402,14 +2948,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng")))) + "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -2443,14 +2989,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.24.0") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp")))) + "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -2467,14 +3013,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) + "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -2497,13 +3043,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww")))) + "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -2519,13 +3065,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.50.1") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz")))) + "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -2557,13 +3103,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.28.3") + (version "1.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p")))) + "0rqvwhs6d8ls1rq7j5ywl5k0qgblxpzimilyw335bi1yad5s10h3")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -2610,13 +3156,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq")))) + "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -2638,14 +3184,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz")))) + "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -2680,13 +3226,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi")))) + "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -2711,14 +3257,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427")))) + "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -2742,13 +3288,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g")))) + "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2788,14 +3334,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) + "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -2814,20 +3360,21 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn")))) + "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs (list r-circlize r-clue + r-codetools r-colorspace r-digest r-doparallel @@ -2853,14 +3400,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy")))) + "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -2924,14 +3471,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9")))) + "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -2962,14 +3509,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1")))) + "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -3007,13 +3554,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "1yc9mlc0ifb7h6rzskq97bsdq1kwdp5qq9l9mciwyxf6yjkmv5ni")))) + (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -3045,14 +3592,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6")))) + "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -3072,14 +3619,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-edaseq (package (name "r-edaseq") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7")))) + "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -3112,13 +3659,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.36.0") + (version "3.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk")))) + "1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -3137,14 +3684,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.18.2") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx")))) + "183rs74ngfvn9xz36csch495pqaash90yhhikm73m7b2bc37ziwz")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -3182,14 +3729,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) + "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges @@ -3209,14 +3756,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) + "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -3237,14 +3784,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) + "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -3261,13 +3808,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) + "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-gplots)) @@ -3280,13 +3827,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) + "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -3327,13 +3874,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.30.0") + (version "1.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns")))) + "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -3354,13 +3901,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9")))) + "1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -3387,13 +3934,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.46.3") + (version "1.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk")))) + "18ain5s0ry6w0ki4c0czvwax2ncigrldyac30a6mlbzyaga6i54h")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -3431,14 +3978,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.30.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x")))) + "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -3465,13 +4012,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.46.1") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx")))) + "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -3492,14 +4039,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z")))) + "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -3523,14 +4070,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6")))) + "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -3552,14 +4099,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) + "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3572,14 +4119,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4")))) + "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -3601,13 +4148,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) + "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -3621,14 +4168,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab")))) + "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -3646,14 +4193,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279")))) + "0hzlm6nzmx0iyjh063512a3ghc1xqb58g5z2bnd2wl4y42iww7bg")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -3667,16 +4214,37 @@ Shiny-based display methods for Bioconductor objects.") @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") (license license:artistic2.0))) +(define-public r-lfa + (package + (name "r-lfa") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "lfa" version)) + (sha256 + (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l")))) + (properties `((upstream-name . "lfa"))) + (build-system r-build-system) + (propagated-inputs (list r-corpcor)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/StoreyLab/lfa") + (synopsis "Logistic Factor Analysis for categorical data") + (description + "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on +Binomial data via estimation of latent structure in the natural parameter.") + (license license:gpl3))) + (define-public r-limma (package (name "r-limma") - (version "3.50.0") + (version "3.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy")))) + "193l3z2jv0kr91nl4r64p3jzb2rai9k8akx1zw7303nsnwpiiaay")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -3689,13 +4257,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx")))) + "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -3763,14 +4331,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) + "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3809,14 +4377,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.20.1") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0ip614mdwisz2hlmyfgngysq1s3hajb88cgdmygfc8i6kyxjkjzl")))) + "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -3854,14 +4422,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p")))) + "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -3911,14 +4479,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri")))) + "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -3942,19 +4510,17 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1")) + "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds")) (modules '((guix build utils))) (snippet - '(begin - (delete-file-recursively "src/boost") - #t)))) + '(delete-file-recursively "src/boost")))) (properties `((upstream-name . "mzR"))) (build-system r-build-system) (arguments @@ -3968,12 +4534,9 @@ specific parser.") (("\\ARCH_OBJS=" line) (string-append line "\nBOOST_LIBS=-lboost_system -lboost_regex \ --lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) - #t))))) +-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))))))) (inputs - (list ;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.28.0. - boost-for-mysql ; use this instead of the bundled boost sources + (list boost ; use this instead of the bundled boost sources zlib)) (propagated-inputs (list r-biobase @@ -3981,8 +4544,7 @@ specific parser.") r-ncdf4 r-protgenerics r-rcpp - r-rhdf5lib - r-zlibbioc)) + r-rhdf5lib)) (native-inputs (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") @@ -3999,14 +4561,14 @@ previously been used in XCMS.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83")))) + "1xklaiyd4mv9sf9211flq1s68fhdn53y2i4l1k2ib39a4l6y9cyr")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -4031,14 +4593,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.86.0") + (version "1.88.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg")))) + "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -4055,17 +4617,59 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; r-aroma-light, r-dnacopy.. +(define-public r-pscbs + (package + (name "r-pscbs") + (version "0.66.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PSCBS" version)) + (sha256 + (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) + (properties `((upstream-name . "PSCBS"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-aroma-light + r-dnacopy + r-future + r-listenv + r-matrixstats + r-r-cache + r-r-methodss3 + r-r-oo + r-r-utils)) + (native-inputs + (list r-r-rsp ;used to build vignettes + r-r-devices)) + (home-page "https://github.com/HenrikBengtsson/PSCBS") + (synopsis "Analysis of parent-specific DNA copy numbers") + (description + "This is a package for segmentation of allele-specific DNA copy number +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-protgenerics (package (name "r-protgenerics") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0")))) + "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -4078,14 +4682,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0")))) + "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -4100,13 +4704,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7")))) + "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -4150,14 +4754,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6")))) + "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -4181,14 +4785,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7")))) + "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -4231,13 +4835,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) + "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) @@ -4258,14 +4862,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78")))) + "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs @@ -4284,13 +4888,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh")))) + "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -4349,13 +4953,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc")))) + "1d9sak1xrrkcvj0q3vnp6w2k0nx2k2ajhsbq0dyb4nhcghp5w8fd")))) (build-system r-build-system) (arguments `(#:phases @@ -4428,13 +5032,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "08jq04ckjw8a5y753almc5bl8vnn4j6qp2zb7bb9w3ql3ddy7b21")))) + (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs @@ -4465,13 +5069,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd")))) + (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -4481,9 +5085,14 @@ cell types based on specific research needs.") r-biocsingular r-bluster r-delayedarray + r-genomeinfodb + r-genomicranges r-igraph + r-iranges r-mass r-matrix + r-rsamtools + r-rtracklayer r-s4vectors r-scater r-scran @@ -4502,17 +5111,59 @@ includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.") (license license:gpl3))) +(define-public r-scmap + (package + (name "r-scmap") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scmap" version)) + (sha256 + (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (properties `((upstream-name . "scmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dplyr + r-e1071 + r-ggplot2 + r-googlevis + r-matrixstats + r-proxy + r-randomforest + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hemberg-lab/scmap") + (synopsis "Tool for unsupervised projection of single cell RNA-seq data") + (description + "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the +composition of complex tissues since the technology allows researchers to +define cell-types using unsupervised clustering of the transcriptome. +However, due to differences in experimental methods and computational +analyses, it is often challenging to directly compare the cells identified in +two different experiments. @code{scmap} is a method for projecting cells from +a scRNA-seq experiment onto the cell-types or individual cells identified in a +different experiment.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl")))) + "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs @@ -4528,13 +5179,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na")))) + "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -4551,14 +5202,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx")))) + "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -4594,14 +5245,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98")))) + "1g3kfa17p60jkk4l34vc5hdq83w082qsxbjvpqw7r9rdd8d79z2q")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -4611,9 +5262,11 @@ ungapped alignment formats.") r-circlize r-clue r-cluster + r-colorspace r-complexheatmap r-digest r-getoptlong + r-globaloptions r-go-db r-gosemsim r-matrix @@ -4633,13 +5286,13 @@ and comparing the clusterings.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy")))) + (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs @@ -4683,14 +5336,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1")))) + "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -4710,13 +5363,13 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) + "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -4739,16 +5392,39 @@ events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) +(define-public r-stager + (package + (name "r-stager") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "stageR" version)) + (sha256 + (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y")))) + (properties `((upstream-name . "stageR"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/stageR") + (synopsis "Stage-wise analysis of high throughput gene expression data") + (description + "The stageR package allows automated stage-wise analysis of +high-throughput gene expression data. The method is published in Genome +Biology at +@url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.") + (license license:gpl3))) + (define-public r-stringdb (package (name "r-stringdb") - (version "2.6.0") + (version "2.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm")))) + (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -4775,13 +5451,13 @@ that integrates the various evidences.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678")))) + (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -4812,13 +5488,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a")))) + "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -4846,14 +5522,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.42.0") + (version "3.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) + "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4")))) (build-system r-build-system) (propagated-inputs (list r-edger @@ -4877,14 +5553,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.0.5") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf")))) + "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -4920,13 +5596,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2")))) + "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -4953,13 +5629,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) + "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -5010,13 +5686,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.40.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva")))) + "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -5048,14 +5724,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.62.0") + (version "3.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) + "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) @@ -5077,16 +5753,53 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) +;; There is no source tarball, so we fetch the code from the Bioconductor git +;; repository. +(define-public r-xcir + (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277") + (revision "1")) + (package + (name "r-xcir") + (version (git-version "1.8.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.bioconductor.org/packages/XCIR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p")))) + (properties `((upstream-name . "XCIR"))) + (build-system r-build-system) + (propagated-inputs (list r-biomart + r-biostrings + r-data-table + r-ggplot2 + r-iranges + r-readxl + r-s4vectors + r-seqminer + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/SRenan/XCIR") + (synopsis "Analysis of X chromosome inactivation") + (description + "This package is an R package that offers models and tools for subject +level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape +inference.") + (license license:gpl2)))) + (define-public r-xina (package (name "r-xina") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp")))) + (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs @@ -5116,13 +5829,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi")))) + (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") @@ -5143,13 +5856,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0")))) + "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -5177,13 +5890,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj")))) + "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -5196,13 +5909,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.4.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg")))) + (base32 "1w3qi35vk289cpky1pb0wgg1hr55s5kdw7np98i9c1vmwi3gvwr7")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -5228,14 +5941,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) + "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -5253,14 +5966,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264")))) + "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -5288,14 +6001,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) + "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -5324,14 +6037,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) + "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -5378,13 +6091,13 @@ integration with @code{Rcpp}.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr")))) + "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -5405,13 +6118,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv")))) + "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -5432,14 +6145,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.4.3") + (version "3.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj")))) + "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -5510,13 +6223,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) + "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -5542,14 +6255,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) + "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase r-mass)) @@ -5577,13 +6290,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) + "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) @@ -5670,14 +6383,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b")))) + "1ch636j3zd6hcfnl455vjs36wffrdhwzyvkbikcwjg7idiknjdkf")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -5724,13 +6437,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3")))) + "0s7s39v9lqniirjgp8lbmffw0c8rsp6bndgzy1zlyh5vivfih0f5")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -5751,12 +6464,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) + (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i")))) (build-system r-build-system) (propagated-inputs (list r-limma)) @@ -5770,12 +6483,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d")))) + (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -5789,12 +6502,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr")))) + (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -5808,12 +6521,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj")))) + (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -5840,14 +6553,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r")))) + "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -5864,14 +6577,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq")))) + "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -5898,14 +6611,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx")))) + "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -5939,14 +6652,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd")))) + "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -5967,14 +6680,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw")))) + "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -6001,14 +6714,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb")))) + "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -6042,14 +6755,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) + "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") @@ -6062,14 +6775,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) + "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -6088,14 +6801,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9")))) + "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -6121,14 +6834,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki")))) + "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -6144,14 +6857,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) + "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) @@ -6168,14 +6881,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk")))) + "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -6214,14 +6927,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg")))) + "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -6241,14 +6954,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q")))) + "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -6266,14 +6979,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr")))) + "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -6294,14 +7007,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc")))) + "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -6320,14 +7033,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "19i8jhvycv57zbxhpn5gx5ymdiws64kc3nidc00xh1j9a8xkj1aq")))) + "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -6352,14 +7065,14 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.2.1") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0qk39gdpy4kznjhmvi25y2spcdj2r1i6mv673vx8dzf66zfs20v8")))) + "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -6389,14 +7102,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk")))) + "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -6418,14 +7131,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n")))) + "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -6453,14 +7166,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.8.0") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y")))) + "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -6486,7 +7199,7 @@ possible, parallelization is achieved using the BiocParallel framework.") r-tidyselect r-vim)) (native-inputs - (list r-nbconvertr)) ; for vignettes + (list r-knitr r-nbconvertr)) ; for vignettes (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion @@ -6497,14 +7210,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky")))) + "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -6519,14 +7232,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk")))) + "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -6559,13 +7272,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) + "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) @@ -6579,14 +7292,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) + "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -6677,14 +7390,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m")))) + "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -6699,13 +7412,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) + "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -6737,14 +7450,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) + "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) (build-system r-build-system) (inputs (list zlib)) @@ -6766,14 +7479,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx")))) + "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -6795,14 +7508,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.22.2") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy")))) + "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -6810,6 +7523,7 @@ independent of the p-value under the null hypothesis.") r-dt r-ggplot2 r-limma + r-markdown r-reshape2 r-rocr r-scales @@ -6831,14 +7545,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg")))) + "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -6860,14 +7574,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr")))) + "1zyvjr9nwfh0cdqk4kwmr30yhh05picyab1hpnpn737xvn525jfi")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -6903,14 +7617,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy")))) + "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs @@ -6938,14 +7652,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) + "1fyqd7qhij2iyx9vdmgnx2qf0w3kwbkmg805539zrmxry8cwfldb")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -6954,13 +7668,13 @@ single cell assay data.") r-cluster r-combinat r-ddrtree - r-densityclust r-dplyr r-fastica r-ggplot2 r-hsmmsinglecell r-igraph r-irlba + r-leidenbase r-limma r-mass r-matrix @@ -6993,11 +7707,11 @@ qPCR data, but could be used with other types as well.") (license license:artistic2.0))) (define-public r-leidenbase - (let ((commit "430f22af6982cc7d2e6e77f6b0df47bc970dcbce") + (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96") (revision "1")) (package (name "r-leidenbase") - (version (git-version "0.1.3" revision commit)) + (version (git-version "0.1.9" revision commit)) (source (origin (method git-fetch) @@ -7007,7 +7721,7 @@ qPCR data, but could be used with other types as well.") (file-name (git-file-name name version)) (sha256 (base32 - "0ylqsmdpv4xq6f6ldxvwkhk33a9i1jcgk60zvksk3iplykfzd6c0")))) + "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f")))) (properties `((upstream-name . "leidenbase"))) (build-system r-build-system) (inputs @@ -7123,14 +7837,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v")))) + "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -7149,14 +7863,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5")))) + "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -7187,14 +7901,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) + "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light @@ -7231,21 +7945,21 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.62.1") + (version "2.64.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0plmh4x37r848g6ilvl1x8cim90rp85gikfc5m8lgi2i4xkq7hbq")))) + "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-curl r-data-table r-dplyr - r-httr r-limma r-magrittr r-r-utils @@ -7266,14 +7980,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.36.0") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) + "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62")))) (build-system r-build-system) (propagated-inputs (list r-base64)) @@ -7287,14 +8001,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) + "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) @@ -7311,14 +8025,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) + "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -7345,14 +8059,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) + "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6")))) (build-system r-build-system) (propagated-inputs (list r-beanplot @@ -7396,14 +8110,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.40.1") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) + "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -7443,14 +8157,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) + "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -7482,14 +8196,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj")))) + "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -7543,14 +8257,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h")))) + "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -7634,13 +8348,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) + "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -7703,14 +8417,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl")))) + "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -7743,14 +8457,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf")))) + "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -7768,14 +8482,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab")))) + "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -7795,14 +8509,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) + "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) @@ -7825,14 +8539,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9")))) + "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -7847,13 +8561,13 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd")))) + (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs @@ -7880,14 +8594,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) + "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg")))) (build-system r-build-system) (propagated-inputs (list r-bh @@ -7912,14 +8626,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.20.1") + (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n")))) + "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -7947,14 +8661,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.14.1") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) + "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -7985,14 +8699,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.2.1") + (version "4.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4")))) + "03bg3agisrm4q10gg57dksvd1ws37if6a1gwcxaybb4c50zadm8p")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -8022,13 +8736,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) + "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -8068,14 +8782,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag")))) + "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -8110,14 +8824,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l")))) + "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq")))) (build-system r-build-system) (arguments `(#:phases @@ -8142,14 +8856,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0")))) + "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -8166,14 +8880,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb")))) + "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -8196,14 +8910,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d")))) + "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -8220,14 +8934,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr")))) + "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -8244,14 +8958,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy")))) + "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -8275,14 +8989,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) + "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -8296,14 +9010,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz")))) + "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -8344,14 +9058,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) + "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) @@ -8369,14 +9083,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v")))) + "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -8423,12 +9137,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425")))) + (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -8450,12 +9164,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj")))) + (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -8465,7 +9179,6 @@ frequency matrices from nine public sources, for multiple organisms.") r-bsgenome r-genomeinfodb r-genomicranges - r-grimport r-gviz r-iranges r-matrixstats @@ -8501,18 +9214,23 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz")))) + "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs - (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml)) + (list r-ade4 + r-biostrings + r-ggplot2 + r-htmlwidgets + r-tfbstools + r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/motifStack/") @@ -8528,14 +9246,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls")))) + "0zq9k4189dlc14f9rknsc1ffhpjzb2f4fzdaszfdbnd4rr43b79i")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -8565,14 +9283,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.18.0") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn")))) + "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -8612,14 +9330,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127")))) + "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -8717,14 +9435,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh")))) + "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -8742,14 +9460,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq")))) + "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -8785,23 +9503,24 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp")))) + "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-data-table + r-delayedarray + r-delayedmatrixstats r-gseabase r-mixtools r-r-utils - r-s4vectors r-shiny r-summarizedexperiment)) (native-inputs @@ -8824,14 +9543,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.36.0") + (version "4.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619")))) + "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -8863,14 +9582,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) + "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -8896,14 +9615,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) + "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) @@ -8922,14 +9641,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql")))) + "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -8961,14 +9680,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h")))) + "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -9010,14 +9729,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) + "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -9092,14 +9811,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) + "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -9125,14 +9844,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) + "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -9162,14 +9881,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) + "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -9230,19 +9949,19 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4")))) + "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) - (propagated-inputs - (list r-waveslim)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description @@ -9254,14 +9973,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.16.1") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143")))) + "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -9292,17 +10011,58 @@ imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses data for high-throughput, untargeted analyte profiling.") (license license:gpl2+))) +(define-public r-wppi + (package + (name "r-wppi") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "wppi" version)) + (sha256 + (base32 + "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f")))) + (properties `((upstream-name . "wppi"))) + (build-system r-build-system) + ;; This is necessary because omnipathr attempts to write a configuration + ;; file to HOME. + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs (list r-dplyr + r-igraph + r-logger + r-magrittr + r-matrix + r-omnipathr + r-progress + r-purrr + r-rcurl + r-rlang + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/AnaGalhoz37/wppi") + (synopsis "Weighting protein-protein interactions") + (description + "This package predicts functional relevance of protein-protein +interactions based on functional annotations such as Human Protein Ontology +and Gene Ontology, and prioritizes genes based on network topology, functional +scores and a path search algorithm.") + (license license:expat))) + (define-public r-wrench (package (name "r-wrench") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n")))) + "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -9319,14 +10079,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) + "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -9353,14 +10113,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j")))) + "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -9374,14 +10134,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) + "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah")))) (build-system r-build-system) (inputs (list netpbm perl)) @@ -9406,14 +10166,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) + "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -9439,14 +10199,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9")))) + "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -9464,14 +10224,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x")))) + "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -9491,21 +10251,23 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) + "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b")))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-decoupler r-dplyr r-ggplot2 r-ggrepel r-gridextra + r-reshape2 r-tidyr)) (native-inputs (list r-knitr)) @@ -9521,14 +10283,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh")))) + "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -9544,14 +10306,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1")))) + "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -9577,14 +10339,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) + "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -9607,16 +10369,28 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr")))) + "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) + (arguments + `(#:phases + ;; Disable unsupported `popcnt' instructions on + ;; architectures other than x86_64 + ,(if (string-prefix? "x86_64" + (or (%current-target-system) + (%current-system))) + '%standard-phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-sources + (lambda _ + (setenv "POPCNT_CAPABILITY" "0"))))))) (inputs (list zlib)) (native-inputs (list r-knitr)) @@ -9631,14 +10405,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja")))) + "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -9674,14 +10448,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y")))) + "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -9712,14 +10486,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5")))) + "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -9754,14 +10528,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071")))) + "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -9797,18 +10571,18 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w")))) + "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs - (list r-igraph r-matrix r-slam r-tsne)) + (list r-igraph r-matrix r-rtsne r-slam)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description @@ -9850,14 +10624,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s")))) + "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -9887,14 +10661,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) + "1i9g32mjknrd2lbz2nisc7nr0gk9byx9aik1i7xdwmq4ndxf8rf7")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multidataset)) @@ -9924,14 +10698,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) + "11w28nlz0f06idbna5k9xs891w516401l1zab5gg7s0z3xxaki4f")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls)) @@ -9953,14 +10727,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) + "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -9994,14 +10768,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.8.1") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn")))) + "1cf80gmzz4c1pvif3350ifsmsbfplyl2na39n8g3x0zkwpl6ijdc")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -10020,14 +10794,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.58.0") + (version "1.59.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161")))) + "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs @@ -10046,14 +10820,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr")))) + "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -10066,17 +10840,60 @@ and to both short and long sequence reads.") cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) +;; This is the latest commit and it solves a bug from the latest release. +(define-public r-cycombine + (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1")) + (package + (name "r-cycombine") + (version (git-version "0.2.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biosurf/cyCombine") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm")))) + (properties `((upstream-name . "cyCombine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-cytolib + r-dplyr + r-flowcore + r-ggplot2 + r-knitr + r-kohonen + r-magrittr + r-purrr + r-rcolorbrewer + r-readr + r-readxl + r-stringr + r-sva + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/biosurf/cyCombine") + (synopsis "Integration of single-cell cytometry datasets") + (description + "This package provides a method for combining single-cell cytometry +datasets, which increases the analytical flexibility and the statistical power +of the analyses while minimizing technical noise.") + (license license:expat)))) + (define-public r-cytolib (package (name "r-cytolib") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9")))) + "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs @@ -10098,14 +10915,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp")))) + "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -10130,14 +10947,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6")))) + "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -10153,14 +10970,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar")))) + "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs @@ -10184,14 +11001,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1")))) + "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -10221,14 +11038,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04")))) + "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -10252,14 +11069,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.32.0") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi")))) + "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -10268,13 +11085,8 @@ statistics to the plot.") (propagated-inputs (list r-biobase r-biocgenerics - r-clue - r-corpcor - r-ellipse r-flowcore - r-flowviz - r-graph - r-mnormt)) + r-graph)) (inputs (list gsl)) (native-inputs @@ -10291,14 +11103,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10")))) + "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -10307,7 +11119,7 @@ model with Box-Cox transformation.") (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" - (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) + (invoke "tar" "xf" "protobuf-3.8.0.tar.gz"))))))) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/RProtoBufLib/") @@ -10320,14 +11132,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.6.0") + (version "4.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig")))) + "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -10374,20 +11186,21 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.6.0") + (version "4.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9")))) + "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-cluster + r-corpcor r-fda r-flowcore r-flowviz @@ -10396,6 +11209,7 @@ matches the flowJo analysis.") r-ks r-lattice r-mass + r-mnormt r-ncdfflow r-rcolorbrewer r-rrcov)) @@ -10410,14 +11224,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm")))) + "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -10454,14 +11268,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz")))) + "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -10506,14 +11320,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f")))) + "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -10549,14 +11363,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.18.1") + (version "6.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f")))) + "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -10595,14 +11409,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9")))) + "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -10641,14 +11455,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7")))) + "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -10657,11 +11471,11 @@ data, to only emphasize the data that actually matters.") r-biocgenerics r-data-table r-dplyr - r-feather r-genomeinfodb r-genomicranges r-gseabase r-r-utils + r-s4vectors r-summarizedexperiment r-tibble)) (native-inputs @@ -10683,14 +11497,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn")))) + "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs @@ -10705,14 +11519,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) + "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -10772,14 +11586,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf")))) + "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -10907,14 +11721,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw")))) + "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs @@ -10931,14 +11745,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9")))) + "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs @@ -10950,43 +11764,17 @@ regulatory networks from expression data.") Characteristic} (ROC) curves, with a focus on micro arrays.") (license license:artistic2.0))) -(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 - (package - (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") - (version "0.6.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri - "IlluminaHumanMethylation450kanno.ilmn12.hg19" - version 'annotation)) - (sha256 - (base32 - "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) - (properties - `((upstream-name - . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) - (build-system r-build-system) - (propagated-inputs (list r-minfi)) - (home-page - "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") - (synopsis "Annotation for Illumina's 450k methylation arrays") - (description - "This package provides manifests and annotation for Illumina's 450k array -data.") - (license license:artistic2.0))) - (define-public r-watermelon (package (name "r-watermelon") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3")))) + "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -11017,14 +11805,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp")) + "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -11073,14 +11861,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali")))) + "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -11104,14 +11892,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr")))) + "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -11125,55 +11913,17 @@ and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) -(define-public r-snplocs-hsapiens-dbsnp144-grch37 - (package - (name "r-snplocs-hsapiens-dbsnp144-grch37") - (version "0.99.20") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" - version 'annotation)) - (sha256 - (base32 - "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - (list r-biocgenerics - r-s4vectors - r-iranges - r-genomeinfodb - r-genomicranges - r-bsgenome - r-biostrings)) - (home-page - "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") - (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") - (description "This package provides SNP locations and alleles for Homo -sapiens extracted from NCBI dbSNP Build 144. The source data files used for -this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped -to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a -patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, -X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for -the mitochondrion chromosome. Therefore, the SNPs in this package can be -injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the -correct position but this injection will exclude chrM (i.e. nothing will be -injected in that sequence).") - (license license:artistic2.0))) - (define-public r-reqon (package (name "r-reqon") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1")))) + "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -11189,14 +11939,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk")))) + "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -11236,14 +11986,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d")))) + "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -11277,14 +12027,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p")))) + "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -11383,19 +12133,20 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw")))) + "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-aod + r-biobase r-biocparallel r-doparallel r-foreach @@ -11409,7 +12160,9 @@ arrays based on fast wavelet-based functional models.") r-matrix r-pbkrtest r-progress + r-rdpack r-reshape2 + r-rhpcblasctl r-rlang r-scales)) (native-inputs @@ -11428,14 +12181,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3")))) + "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -11458,14 +12211,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk")))) + "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -11482,14 +12235,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg")))) + "0n2msyyy1xhapkd66j4xwabg4qfd62l01p1nmafjwifnjsx45xvp")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -11527,6 +12280,111 @@ enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.") (license license:gpl3))) +(define-public r-ace + (package + (name "r-ace") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ACE" version)) + (sha256 + (base32 + "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m")))) + (properties `((upstream-name . "ACE"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tgac-vumc/ACE") + (synopsis + "Absolute copy number estimation from low-coverage whole genome sequencing") + (description + "This package uses segmented copy number data to estimate tumor cell +percentage and produce copy number plots displaying absolute copy numbers. For +this it uses segmented data from the @code{QDNAseq} package, which in turn uses +a number of dependencies to turn mapped reads into segmented data. @code{ACE} +will run @code{QDNAseq} or use its output rds-file of segmented data. It will +subsequently run through all samples in the object(s), for which it will create +individual subdirectories. For each sample, it will calculate how well the +segments fit (the relative error) to integer copy numbers for each percentage +of @dfn{tumor cells} (cells with divergent segments).") + (license license:gpl2))) + +(define-public r-acgh + (package + (name "r-acgh") + (version "1.74.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "aCGH" version)) + (sha256 + (base32 + "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d")))) + (properties `((upstream-name . "aCGH"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) + (home-page "https://bioconductor.org/packages/aCGH") + (synopsis + "Classes and functions for array comparative genomic hybridization data") + (description + "This package provides functions for reading +@dfn{array comparative genomic hybridization} (aCGH) data from image analysis +output files and clone information files, creation of @code{aCGH} objects for +storing these data. Basic methods are accessing/replacing, subsetting, +printing and plotting @code{aCGH} objects.") + (license license:gpl2))) + +(define-public r-acme + (package + (name "r-acme") + (version "2.52.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ACME" version)) + (sha256 + (base32 + "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25")))) + (properties `((upstream-name . "ACME"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-biocgenerics)) + (home-page "https://bioconductor.org/packages/aCGH/") + (synopsis "Calculating microarray enrichment") + (description + "This package implements @dfn{algorithms for calculating microarray +enrichment} (ACME), and it is a set of tools for analysing tiling array of +@dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip), +DNAse hypersensitivity, or other experiments that result in regions of the +genome showing enrichment. It does not rely on a specific array technology +(although the array should be a tiling array), is very general (can be applied +in experiments resulting in regions of enrichment), and is very insensitive to +array noise or normalization methods. It is also very fast and can be applied +on whole-genome tiling array experiments quite easily with enough memory.") + (license license:gpl2+))) + +(define-public r-acde + (package + (name "r-acde") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "acde" version)) + (sha256 + (base32 + "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2")))) + (properties `((upstream-name . "acde"))) + (build-system r-build-system) + (propagated-inputs (list r-boot)) + (home-page "https://bioconductor.org/packages/acde") + (synopsis + "Identification of differentially expressed genes with artificial components") + (description + "This package provides a multivariate inferential analysis method for +detecting differentially expressed genes in gene expression data. It uses +artificial components, close to the data's principal components but with an +exact interpretation in terms of differential genetic expression, to identify +differentially expressed genes while controlling the @dfn{false discovery +rate} (FDR).") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs @@ -11570,14 +12428,14 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1prhwx0nnwy2q62l2r0z31mhk4mq6xdr6mjihdlwpwgwq4rfi60y")))) + "0zbrgz91mlik7j8j11wsdswqqqfsijj8jkgd5fx1ar3mc6rqsmbg")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) @@ -11598,14 +12456,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn")))) + "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs @@ -11620,14 +12478,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm")))) + "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs @@ -11642,14 +12500,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2")))) + "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -11668,14 +12526,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6")))) + "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -11690,14 +12548,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk")))) + "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -11719,14 +12577,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2")))) + "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -11745,14 +12603,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf")))) + "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -11767,14 +12625,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) + "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) @@ -11789,14 +12647,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr")))) + "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -11853,14 +12711,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q")))) + "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs @@ -11896,14 +12754,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.46.0") + (version "3.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8")))) + "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -11939,13 +12797,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0")))) + (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs @@ -11968,14 +12826,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i")))) + "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -12003,14 +12861,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r")))) + "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -12032,18 +12890,18 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr")))) + "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs)) + (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -12055,14 +12913,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b")))) + "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -12087,14 +12945,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6")))) + "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -12131,13 +12989,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y")))) + "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -12146,7 +13004,6 @@ monograph.") r-graph r-httr r-knitr - r-optparse r-biocmanager r-biocviews r-stringdist)) @@ -12161,14 +13018,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq")))) + "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -12183,13 +13040,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd")))) + "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -12207,13 +13064,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.62.1") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r")))) + "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -12235,14 +13092,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq")))) + "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -12269,14 +13126,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s")))) + "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -12296,14 +13153,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9")))) + "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -12331,14 +13188,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9")))) + "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -12376,14 +13233,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq")))) + "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -12403,14 +13260,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1yz2sgx4xrnw22k3d6q6hkj213bnbb4hbr5ymxnmjnsz551s75ny")))) + "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -12451,14 +13308,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1x5ar9byr85iap2x6y66j31fi17wr31awx1gl3z01sckp0dldx6w")))) + "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -12489,14 +13346,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa")))) + "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -12522,14 +13379,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp")))) + "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -12544,14 +13401,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4")))) + "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -12590,14 +13447,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl")))) + "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs @@ -12614,14 +13471,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh")))) + "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -12647,14 +13504,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs")))) + "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -12770,14 +13627,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x")))) + "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -12791,13 +13648,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.32.3") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw")))) + "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -12820,14 +13677,14 @@ S4Vectors package itself.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.70-3") + (version "1.71") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r")))) + "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -12858,14 +13715,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7")))) + "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -12896,13 +13753,13 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y")))) + "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -12920,13 +13777,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx")))) + "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -12949,14 +13806,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4")))) + "0s9vj74359ckmwl8r951jxrzkidslwdl9qamkhz8ilw8b5awxyw4")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -12980,22 +13837,21 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.16.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p")) + "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries (delete-file-recursively "src/wininclude/") - (delete-file-recursively "src/winlib-8.3.0/") - (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz") - #t)))) + (delete-file-recursively "src/winlib/") + (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz"))))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) (arguments @@ -13004,11 +13860,8 @@ block processing.") (add-after 'unpack 'do-not-use-bundled-hdf5 (lambda* (#:key inputs #:allow-other-keys) (for-each delete-file '("configure" "configure.ac")) - ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - ((" \"%s/libsz.a\"") "") - (("patharch, .getDynamicLinks") - ".getDynamicLinks")) + (("return\\(links\\)") "return(\" -lz\")")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -13027,6 +13880,8 @@ block processing.") "hdf5/src/libhdf5.settings") (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" + (("@BUILD_HDF5@") "") + (("@COPY_SZIP@") "") (("@ZLIB_LIB@") "-lz") (("@ZLIB_INCLUDE@") "") (("HDF5_CXX_LIB=.*") @@ -13062,14 +13917,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) + "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) @@ -13088,13 +13943,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) + (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) @@ -13136,14 +13991,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g")))) + "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -13182,17 +14037,22 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1s8w3xwwigz803l81bs9cb2dbvvw5r9z8jjcav1rmh9wm8909nfd")))) + (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs - (list r-data-table r-rcolorbrewer r-rhtslib r-survival r-zlibbioc)) + (list r-data-table + r-dnacopy + r-rcolorbrewer + r-rhtslib + r-survival + r-zlibbioc)) (native-inputs (list r-knitr)) (home-page "https://github.com/PoisonAlien/maftools") (synopsis "Summarize, analyze and visualize MAF files") @@ -13206,14 +14066,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z")))) + "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -13240,13 +14100,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk")))) + (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -13287,14 +14147,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39")))) + "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -13315,13 +14175,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "19lsn3cpghkhfbx4jqgbwwrnacrl7vj3r91ymd1gk02c9pn5dmci")))) + (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs @@ -13347,14 +14207,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.4.0") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467")))) + "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -13382,13 +14242,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) + "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -13404,6 +14264,7 @@ of other packages.") r-gridextra r-matrix r-rcolorbrewer + r-rcppml r-rlang r-rtsne r-s4vectors @@ -13423,14 +14284,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic")))) + "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -13466,14 +14327,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1")))) + "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -13491,14 +14352,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk")))) + "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -13527,14 +14388,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv")))) + "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -13556,13 +14417,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq")))) + (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs @@ -13586,14 +14447,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr")))) + "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs @@ -13619,14 +14480,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9")))) + "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -13642,14 +14503,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb")))) + "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -13671,14 +14532,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.18.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi")))) + "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -13710,33 +14571,38 @@ relevant, and the minimum expression of the most abundant condition.") r-summarizedexperiment)) (native-inputs (list r-knitr)) - (home-page - "https://github.com/HelenaLC/CATALYST") + (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") (description - "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass -cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as -reporters to label antibodies, thereby substantially decreasing spectral -overlap and allowing for examination of over 50 parameters at the single cell -level. While spectral overlap is significantly less pronounced in CyTOF than -flow cytometry, spillover due to detection sensitivity, isotopic impurities, -and oxide formation can impede data interpretability. We designed -CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for -preprocessing of cytometry data, including i) normalization using bead -standards, ii) single-cell deconvolution, and iii) bead-based compensation.") + "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass +cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal +isotopes rather than fluorescent tags as reporters to label antibodies, +thereby substantially decreasing spectral overlap and allowing for examination +of over 50 parameters at the single cell level. While spectral overlap is +significantly less pronounced in CyTOF than flow cytometry, spillover due to +detection sensitivity, isotopic impurities, and oxide formation can impede +data interpretability. @code{CATALYST} was designed to provide a pipeline for +preprocessing of cytometry data, including: + +@enumerate +@item normalization using bead standards; +@item single-cell deconvolution; +@item bead-based compensation. +@end enumerate +") (license license:gpl2+))) (define-public r-erma (package (name "r-erma") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) + "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -13769,14 +14635,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7")))) + "1lvms07ba99nzf10gpn50wjca84nj5jrb6902z069p2bfi4xyd27")))) (build-system r-build-system) (arguments `(#:phases @@ -13937,14 +14803,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.38.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8")))) + "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -13986,14 +14852,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.26.0") + (version "2.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) + "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -14020,13 +14886,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4")))) + (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs @@ -14044,14 +14910,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) + "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -14080,14 +14946,14 @@ defining LD blocks.") (define-public r-ldheatmap (package (name "r-ldheatmap") - (version "1.0-4") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "LDheatmap" version)) (sha256 (base32 - "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) + "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc")))) (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs @@ -14106,20 +14972,21 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.6-0") + (version "2.7-1") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "0fr5pyc43hly5ry5bbygibbh9mnql7vl4r5qz42d0ry4hahyxa4w")))) + "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr")))) (build-system r-build-system) (inputs (list gsl)) (propagated-inputs (list r-doparallel r-foreach + r-graph r-lme4 r-nnet r-rcpp @@ -14167,13 +15034,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr")))) + (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -14201,14 +15068,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) + "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) @@ -14225,14 +15092,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1akcmxzn4j9ph4n3lsgfh8fh8hrb28jjamz037w59bsdkcv6wyjq")))) + "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -14263,14 +15130,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9")))) + "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -14295,13 +15162,13 @@ starting site, start codon, stop codon and transcription ending site.") (define-public r-sushi (package (name "r-sushi") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4")))) + "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -14316,14 +15183,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf")))) + "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -14350,14 +15217,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) + "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) @@ -14383,23 +15250,23 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29")))) + "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs (list r-abind r-biocparallel r-data-table + r-dixontest r-futile-logger r-matrix - r-outliers r-rcpp r-rdpack)) (native-inputs @@ -14416,14 +15283,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16")))) + "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs @@ -14452,14 +15319,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk")))) + "093zk43x8i9ajaqsdhndkyal3dizllr3g85ziavb3k73dzvarzsc")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -14486,14 +15353,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s")))) + "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs @@ -14510,14 +15377,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.52.0") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd")))) + "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -14532,14 +15399,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km")))) + "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) @@ -14557,14 +15424,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) + "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) @@ -14581,14 +15448,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99")))) + "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -14605,14 +15472,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a")))) + "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -14631,14 +15498,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39")))) + "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -14665,14 +15532,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w")))) + "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) @@ -14695,14 +15562,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638")))) + "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -14740,14 +15607,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817")))) + "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs @@ -14769,14 +15636,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z")))) + "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -14789,14 +15656,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j")))) + "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -14811,14 +15678,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy")))) + "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs @@ -14836,14 +15703,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p")))) + "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -14892,14 +15759,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg")))) + "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -14921,14 +15788,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8")))) + "0f387j35lj32ryiw48jz8gc08al2lmmv9zvbbgyjq9wmqlca3dfb")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs @@ -14963,14 +15830,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407")))) + "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs @@ -14989,23 +15856,23 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys")))) + "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-genomicranges - r-hmisc r-igraph r-mass r-psych + r-scran r-stringr)) (native-inputs (list r-knitr)) @@ -15019,14 +15886,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g")))) + "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs @@ -15061,14 +15928,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d")))) + "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -15107,14 +15974,14 @@ visualizing bisulfite sequencing data.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd")))) + "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -15153,13 +16020,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8")))) + (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -15189,6 +16056,7 @@ interest on transformed methylation proportions.") r-tibble r-tidyr r-tidyselect + r-withr r-xml2 r-yaml)) (native-inputs (list r-knitr)) @@ -15205,14 +16073,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj")))) + "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -15230,6 +16098,7 @@ for ligand activity prediction from transcriptomics data.") r-hdf5array r-homo-sapiens r-impute + r-iranges r-matrix r-matrixstats r-mus-musculus @@ -15256,13 +16125,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.22.2") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc")))) + (base32 "0kw4lrg8xm0ipj7f7h1rwfj7a8mknkril1pn05x08mx13f7p5p14")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -15308,17 +16177,56 @@ regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.") (license license:gpl3+))) +(define-public r-tricycle + (package + (name "r-tricycle") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tricycle" version)) + (sha256 + (base32 + "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln")))) + (properties `((upstream-name . "tricycle"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-circular + r-dplyr + r-genomicranges + r-ggnewscale + r-ggplot2 + r-iranges + r-rcolorbrewer + r-s4vectors + r-scater + r-scattermore + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hansenlab/tricycle") + (synopsis "Transferable representation and inference of cell cycle") + (description + "The package contains functions to infer and visualize cell cycle process +using Single-cell RNA-Seq data. It exploits the idea of transfer learning, +projecting new data to the previous learned biologically interpretable space. +The @code{tricycle} provides a pre-learned cell cycle space, which could be +used to infer cell cycle time of human and mouse single cell samples. In +addition, it also offer functions to visualize cell cycle time on different +embeddings and functions to build new reference.") + (license license:gpl3))) + (define-public r-tximeta (package (name "r-tximeta") - (version "1.12.4") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g")))) + "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs @@ -15352,13 +16260,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s")))) + (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs |