diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 309 |
1 files changed, 208 insertions, 101 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 00701c4463..bc8eda4293 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1436,6 +1436,51 @@ curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.") (license license:gpl3))) +(define-public r-cellid + (package + (name "r-cellid") + (version "1.8.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CelliD" version)) + (sha256 + (base32 + "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03")))) + (properties `((upstream-name . "CelliD"))) + (build-system r-build-system) + (propagated-inputs + (list r-data-table + r-biocparallel + r-fastmatch + r-fgsea + r-ggplot2 + r-glue + r-irlba + r-matrix + r-matrixstats + r-pbapply + r-rcpp + r-rcpparmadillo + r-reticulate + r-rtsne + r-seurat + r-stringr + r-tictoc + r-singlecellexperiment + r-summarizedexperiment + r-umap)) + (native-inputs (list r-knitr r-scater)) + (home-page "https://bioconductor.org/packages/CelliD") + (synopsis + "Single cell gene signature extraction using multiple correspondence analysis") + (description + "CelliD is a clustering-free method for extracting per-cell gene +signatures from scRNA-seq. CelliD allows unbiased cell identity recognition +across different donors, tissues-of-origin, model organisms and single-cell +omics protocols. The package can also be used to explore functional pathways +enrichment in single cell data.") + (license license:gpl3))) + (define-public r-champdata (package (name "r-champdata") @@ -2814,13 +2859,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1wfbi8xyh2pxpjdv2zhml2l1h8c7fyfl5wyici3nm3rcs00n7m9w")))) + "05gngz6cqihxg4zlf7ymw93qj61a1i19hgp4fkc0cxnkq0pambrd")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -2828,25 +2873,21 @@ analysis, modelling, and visualization of spike-in controls.") r-desctools r-doparallel r-dorng - r-dplyr - r-emmeans r-energy r-foreach + r-gtools r-hmisc r-lme4 r-lmertest - r-magrittr r-mass + r-matrix r-mia + r-multcomp r-nloptr r-rdpack - r-rlang - r-rngtools r-s4vectors r-singlecellexperiment r-summarizedexperiment - r-tibble - r-tidyr r-treesummarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/FrederickHuangLin/ANCOMBC") @@ -3059,13 +3100,13 @@ paired or unpaired study designs.") (define-public r-alevinqc (package (name "r-alevinqc") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "alevinQC" version)) (sha256 (base32 - "014jxp2ymxiywp2qa1b9f7iszgf95v03h9kgk8ljabnbia1zsl67")))) + "137bvqyh1cqmhf9x3xl6n1dv0380lpcr2nxhd60b7zqiw4p14i5a")))) (properties `((upstream-name . "alevinQC"))) (build-system r-build-system) (propagated-inputs @@ -3919,13 +3960,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.2.3") + (version "3.2.5") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "1b5zmyj75fjhyn4mb70gdqvxg76fg2z45vns9l0rl66s3p5mhm6d")))) + "1vqxmz2lknnx1g61y7skvznsnxv3clajngz9mnggg1z3p5mr6cnh")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -4735,13 +4776,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.26.3") + (version "0.26.6") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0m603v0l74nawid61hvqbyb2662c1djqp436p87pk4f04fvws67j")))) + "0jy2spqysa5x1s84kbr1jbbdmlh3q44lrw1qck2fln3b6q5vgz0k")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -5084,13 +5125,13 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.34.0") + (version "2.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "13kmh5zik3gw4jzh666zd3vmv915fcac5lx76s9q38x01m4gd7ld")))) + "013a3vcw1v5vn0sg2d9cwrdksch48kilvxp8cr79y0nr4vk58q9z")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -5112,24 +5153,24 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.21.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "1vzzsqjnkaffyxgvw6bsbxhgg1102cap2hsmzkhwzh6bvh02bwkx")))) + (base32 "1zjwhxlayz2sb77vspw280didhawj282i5gvxnydcdparg165zwf")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics + r-biocparallel r-biostrings r-bsgenome r-dbi r-dexseq r-dplyr - r-drimseq r-edger r-futile-logger r-genomeinfodb @@ -5139,14 +5180,20 @@ possible.") r-iranges r-limma r-magrittr + r-pfamanalyzer r-plyr r-rcolorbrewer r-rcurl r-readr r-reshape2 r-rtracklayer + r-s4vectors + r-saturn r-stringr + r-summarizedexperiment + r-sva r-tibble + r-tidyr r-tximeta r-tximport r-venndiagram @@ -5367,14 +5414,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.78.0") + (version "1.78.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "15hpxflygpy1sid0c4hlzmsc13nqyzs6j74md0ri478qysiqjnpf")))) + "1xj8pnaa782k1hxaiba6mcsqr21bk8xz31916836jz5l9848zjsw")))) (build-system r-build-system) (propagated-inputs (list r-affyio @@ -5605,13 +5652,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.62.1") + (version "1.62.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0a5brfd010p0ks8b7kvrynirmzv3p74r9vqwv5wyz4kbnasfd1v1")))) + "0vprm84k79pfnkkg9vf3gyb1nhzmin5lp5375rsaj6fnzbd46dw9")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -5619,8 +5666,8 @@ microarrays.") (list r-biobase r-biocgenerics r-dbi - r-keggrest r-iranges + r-keggrest r-rsqlite r-s4vectors)) (native-inputs @@ -5660,14 +5707,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.42.0") + (version "1.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0s1k32li3nygg01nv9hbs7n6pabaassxmm4z5jggp6apdzkjpsc7")))) + "0b4dmjv7y50c1rn76wlhnlz93kidvg1byj72vq2s11kdzyq3pmss")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5810,13 +5857,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.56.0") + (version "2.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "10cjysqnc1wr0ld3wjl79zv0irrmxb8hf03y63fbwcc43rjcgv07")))) + "0jqv2mv4ridi5lffva20a5s479bzpxhblyymricb17fd400rag8f")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -5850,13 +5897,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biomartr (package (name "r-biomartr") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "biomartr" version)) (sha256 (base32 - "093v32r6s9sn7yisa4fdwgjif313ap19nvq0sbsgj2482k646d55")))) + "0hv4z6ycmn58ha7j7zfmyhvs2i37cm48gcalg19dli2kaw1c4210")))) (properties `((upstream-name . "biomartr"))) (build-system r-build-system) (propagated-inputs @@ -6377,14 +6424,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.40.1") + (version "1.40.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1910nvcm1lj5mcg8jdvfql6a6h1wnrgfl616gz942g4ngl18ya3p")))) + "0rb6b2aqn3an5ria4yjasjr7aldr5606rkc4yw275x9ddii22djg")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6865,19 +6912,18 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "072dawysgcfyhnwva38y5vf95y3b9dhpad66mwma07hrh27a6wqh")))) + "1c3fgni846vjw152m4aklb8kwrwjw3rww116a2cbii70nr86p5qg")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) (propagated-inputs - (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl - r-s4vectors)) + (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomeInfoDb") @@ -6925,13 +6971,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0sccj6py15g5ihdrpzwn7j71wkqwljay8p2yn2wkd8142cfsr7x3")))) + "166l0pzg00kaagg3adnx1xy5bgmv42lm06a47i30lh14dc0k79wq")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7300,16 +7346,16 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.28.2") + (version "2.0.11") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "0z8aa2435f7v2l6zwv47v2a6p9hal156dsh8v1iri233d1qx7fax")))) + (base32 "0x169fxwlccsqwj1bpviaky3hfr0zdwsdrlgfvrb4j6j95qfgnns")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) - (propagated-inputs (list r-corpcor)) + (propagated-inputs (list r-corpcor r-rspectra)) (native-inputs (list r-knitr)) (home-page "https://github.com/StoreyLab/lfa") (synopsis "Logistic Factor Analysis for categorical data") @@ -7321,13 +7367,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.56.1") + (version "3.56.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "02c559an6hzk00bbvlrq1qljsnby4a53ng9jj6ff570mc6pabjn6")))) + "0miyba9frn1p4pkclzpr0bfazsk0br2jgpwpwwh773d3103hkn0r")))) (build-system r-build-system) (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7340,13 +7386,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-maaslin2 (package (name "r-maaslin2") - (version "1.13.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Maaslin2" version)) (sha256 - (base32 "05xha6y6ssf80l4xb7skbjafpqww2d85l4b6wn72r5djidyxxw6y")))) + (base32 "06mb72hbzihdficv73yqbb2m86bkw78w3vbw1rm98n0npxq2fch6")))) (properties `((upstream-name . "Maaslin2"))) (build-system r-build-system) (propagated-inputs @@ -7363,7 +7409,6 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") r-lme4 r-lmertest r-logging - r-lpsymphony r-mass r-metagenomeseq r-optparse @@ -7372,6 +7417,7 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") r-pheatmap r-pscl r-robustbase + r-tibble r-vegan)) (native-inputs (list r-knitr)) (home-page "http://huttenhower.sph.harvard.edu/maaslin2") @@ -7971,18 +8017,20 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.34.0") + (version "2.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0dz9wqaawhkvswv4035xknlicia0m79r8n666s1yf59cfpmdqgs3")) + "1jsna4xwyph1gg72wwqlpavb65g5nc3db1vmcs1qcw1mdgasdjhk")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) - (properties `((upstream-name . "mzR"))) + (properties + `((upstream-name . "mzR") + (updater-extra-inputs . ("boost")))) (build-system r-build-system) (arguments `(#:phases @@ -8023,13 +8071,13 @@ previously been used in XCMS.") (define-public r-numbat (package (name "r-numbat") - (version "1.3.0") + (version "1.3.2-1") (source (origin (method url-fetch) (uri (cran-uri "numbat" version)) (sha256 (base32 - "0499i20kkpr58b59xmw7d4q4dgp6ryfb9jj55idvhaa2k1kv28n6")))) + "1b9bykgw3z7a8bky5yv2g402gdapv8kcla2kbbyqvs77x4wba4q4")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -8266,6 +8314,29 @@ 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+))) +(define-public r-pfamanalyzer + (package + (name "r-pfamanalyzer") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "pfamAnalyzeR" version)) + (sha256 + (base32 + "0zff887lc4bjrv683kqsw47vjwmf6886wybklsf2wd6hpy23mxfy")))) + (properties `((upstream-name . "pfamAnalyzeR"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/pfamAnalyzeR") + (synopsis "Identification of domain isotypes in pfam data") + (description + "This R package enables the user to read pfam predictions into R. Most +human protein domains exist as multiple distinct variants termed domain +isotypes. This R package enables the identification and classification of such +domain isotypes from pfam data.") + (license license:expat))) + ;; This is a CRAN package, but it depends on a Bioconductor package: ;; r-aroma-light, r-dnacopy.. (define-public r-pscbs @@ -8733,6 +8804,40 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-saturn + (package + (name "r-saturn") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "satuRn" version)) + (sha256 + (base32 + "0frm7iblxkc8ajcdqrfgsvf4krn6x8cr3mx7fnzq06xij0mqm3sj")))) + (properties `((upstream-name . "satuRn"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel + r-boot + r-ggplot2 + r-limma + r-locfdr + r-matrix + r-pbapply + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/statOmics/satuRn") + (synopsis + "Analysis of differential transcript usage for scRNA-seq applications") + (description + "satuRn provides a framework for performing differential transcript usage +analyses. The package consists of three main functions. The first function, +@code{fitDTU}, fits quasi-binomial generalized linear models that model +transcript usage in different groups of interest. The second function, +@code{testDTU}, tests for differential usage of transcripts between groups of +interest. Finally, @code{plotDTU} visualizes the usage profiles of +transcripts in groups of interest.") + (license license:artistic2.0))) + (define-public r-scannotatr (package (name "r-scannotatr") @@ -8819,13 +8924,13 @@ comprehensive scDblFinder method.") (define-public r-scistreer (package (name "r-scistreer") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "scistreer" version)) (sha256 (base32 - "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9")))) + "03nd4p7ik66v09yv18c0z1bvdnkr5m0axk78yapd2ri80ihmyi3c")))) (properties `((upstream-name . "scistreer"))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -9356,13 +9461,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.30.1") + (version "1.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0wj82nmqg9g8663pg5f4h7hqhr1q4ghhiif2p7x1pxmh425sn554")))) + "05dy57fi43rpq9bhbsc4apa62xki99r84098pbvi3rjmac811425")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -9422,14 +9527,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.6.0") + (version "2.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1yg650xkhmp6gcikiiv63g47k1xycg2mj8wxfnihgmlmlw4433yk")))) + "068rikfq32awhvj0abl30bghv5k2z4zlfkbxpmsdapxhmdzhgnba")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -10313,13 +10418,13 @@ fitting of some classes of graphical Markov models.") (define-public r-ggpicrust2 (package (name "r-ggpicrust2") - (version "1.7.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "ggpicrust2" version)) (sha256 (base32 - "0rw2nrmnniff5hb56r21rk0mphba74fppxsa5ps2xamg1a63qfyw")))) + "0a4ykfybwx1qhgn7ic29dzigiazj248iihdr1597jxj505q21gay")))) (properties `((upstream-name . "ggpicrust2"))) (build-system r-build-system) (propagated-inputs (list r-aldex2 @@ -10329,6 +10434,7 @@ fitting of some classes of graphical Markov models.") r-dplyr r-edger r-ggally + r-ggh4x r-ggplot2 r-ggprism r-lefser @@ -10337,7 +10443,6 @@ fitting of some classes of graphical Markov models.") r-metagenomeseq r-microbiomestat r-patchwork - r-phyloseq r-readr r-summarizedexperiment r-tibble @@ -10492,13 +10597,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "17a4gvc1bgiym6z5dy0cigvary4knc4bpmq9bymjlwsg9337b4wg")))) + "1bzdhm2dj93xffla00hphxn45mpyn3cr8nv8d5xjqgx8j136biyy")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -10735,14 +10840,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "15bvjhwh7v4ldg5q52h1y5ks75qw85zynnybcaccypws3zlwvacn")))) + "1vs3mqf3x8zk7p83jkv41kag1bmn5zxrr3j1ldqk6wxsl77h55c5")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -10941,13 +11046,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "05v9lrjbipz9av1gb0x8kd9mkivxy13wjbs5g6rdw3y72gqqv91d")))) + "0d6q8vn8z90k8ffskcn9jmgg5x5pfb3wjv67bqskasy38inn1zg7")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -11627,14 +11732,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "096d0dql1cg85mmxba3dy2a7ba3sxqphsviqqvx1n35xiidsnpyp")))) + "08b4d7k5qx19bpg12pw89ckk8x6r2n28qjdxbmy1cxn6dcgzhijd")))) (build-system r-build-system) (arguments (list @@ -11649,7 +11754,7 @@ coordinates.") (inputs (list zlib)) (native-inputs - (list pkg-config r-knitr)) + (list gfortran pkg-config r-knitr)) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -13574,12 +13679,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.13.7") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0j4i3059n0g9n73nyxaca7pd4hncvgp0ww63i3kyp5pnvwycsax2")))) + (base32 "13fv0rkyb32grswlgzd3zr35p9xpibj2iq62sr23if4w6z5nbml2")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -14929,14 +15034,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.40.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "09k4r5a735022rc33k6a7pr98qxwy8ijsn451hcw18dimqzm78bx")))) + "08vns1wbgpxw1x6djp84f9hl3gqaybbw9917ghfzk0x3ijpvggbg")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -16290,14 +16395,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "10k445cwb5jhgcr0zf85x24mvldwk26zpwh0wq4himr44aha3bwx")) + "11qib2znznzvyb0x9qm1nfg9lhyqy63yrdjicy7n3n6l8dfd2lx7")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -16320,7 +16425,9 @@ metrics, with methods for objects produced by the @code{methylumi} and (substitute* "src/CoreArray/dStream.h" (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) (string-append "include <" header ">"))))))) - (properties `((upstream-name . "gdsfmt"))) + (properties + `((upstream-name . "gdsfmt") + (updater-extra-inputs . ("lz4" "xz" "zlib")))) (build-system r-build-system) (inputs (list lz4 xz zlib)) @@ -16552,14 +16659,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "1j9fkqsxq7z3w2m435lqnrm8d17cd7l4873h26slmxhdazc9n94i")))) + "0v0shsv0s9fzakdb4p84jfc4z57ryan27r1dkbvb3v25kjrhd8fi")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -16658,14 +16765,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.30.0") + (version "1.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "052xay39bzxyn0li631zy2nl08vp7q85q4phigwswpavfhl4w71g")))) + "17jssd327l0miw52iadag2dbk8w4mhv2vwjpzdw89p8gww47bmbv")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -16761,14 +16868,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0v7c624y2sbqs6mc6kd6dynx24zakcilaswssxmplrcx15im87cn")))) + "0v1085dl16a3494f1fxc9rk1ffz3si89mdwbmnnczyhj5p13pfx8")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -17565,13 +17672,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "15f4jx4rkhi6aakdmy23dh3nlb2psaxkvwvrbya9vlsf5lmhajf9")))) + "0a0fnmqln13iglnw8smbbr4k7hdvacipxa04zhqylygpsq1246bc")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -18454,13 +18561,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.6.0") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "0lpafc1770kh4j151509d9lrpfj9jgla14km4vsfrqjmyhf2prss")))) + "0zsw4j6gk25303xpdwnkda2sq3mb4zb4p1mzwiyf7hdyf87zis05")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (propagated-inputs @@ -19088,14 +19195,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0yng347pnsrkbjgfw9xi20ms57kkbdgzh3sz3sj24dp6k0p5s3da")))) + "00jalzg6yphi8ci4iid7x38jlsrvvdswrq7cqa7jybs26ayjldw1")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -19113,14 +19220,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1mjdk76vmjzmmll0r73kfdi3x77hpdbk3jgzdqryxg4gna597q7j")))) + "13iqlw74zh65y2ckwg0b3xbqc6jgj34xjgsg9axfv7j7znwk9igg")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -20258,14 +20365,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "02ai6ybxhj9q9mshkf17ivvqwsh9lhz7fig5wvr3m7a48hmqqg55")))) + "0bg6jfl12jsmhgby7x7g2vfmi61rx0jdksi97hb0zajgh1nvhirh")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -20284,14 +20391,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.10.1") + (version "1.10.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1kmgahjyyrvs475as24yk0jniswjaa507q6zs8zq8jjqa26gy6zj")))) + "1v0qrypdzl1bg85k8i7qamb6709cgk4ypmisjh6bn5r36nqd5qx4")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -20489,14 +20596,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.8.0") + (version "1.8.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0733v4mijf94gn0sbkhiinb3hxlsfqw2l89gx94k88sp3qy2qzvc")))) + "0nrvq6cn55qzp66pqssyfxl2wh5dfqndchcv8qgfqajsnz8i35xm")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -20504,8 +20611,8 @@ using aCGH or sequencing.") r-complexheatmap r-dynamictreecut r-genie3 + r-ggdendro r-ggnetwork - r-ggnewscale r-ggplot2 r-ggrepel r-igraph @@ -20513,10 +20620,10 @@ using aCGH or sequencing.") r-matrixstats r-minet r-netrep - r-networkd3 r-patchwork r-rcolorbrewer r-reshape2 + r-rlang r-summarizedexperiment r-sva r-wgcna)) @@ -20982,13 +21089,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.28.2") + (version "2.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "16hpljnqskgv7mycj0ipfxhvkyy0hcqvnrn5m416plwcx5cj2fjm")))) + (base32 "1hh09ya4jg062k1ibp1cpvdrgv6gwr95ch57iycgd3cjc5g0xhii")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs |