diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 465 |
1 files changed, 376 insertions, 89 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c62c5970b8..53c7d048c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2202,6 +2202,53 @@ conditions or various species. @code{AMOUNTAIN} aims to search active modules in multi-layer WGCN using a continuous optimization approach.") (license license:gpl2+))) +(define-public r-amplican + (package + (name "r-amplican") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "amplican" version)) + (sha256 + (base32 + "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij")))) + (properties `((upstream-name . "amplican"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-biostrings + r-clustercrit + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggthemes + r-gridextra + r-gtable + r-iranges + r-knitr + r-matrix + r-matrixstats + r-rcpp + r-rmarkdown + r-s4vectors + r-shortread + r-stringr + r-waffle)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/valenlab/amplican") + (synopsis "Automated analysis of CRISPR experiments") + (description + "The package performs alignment of the amplicon reads, normalizes +gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) +and presents the results in the form of aggregated reports. Data and +statistics can be broken down by experiments, barcodes, user defined groups, +guides and amplicons allowing for quick identification of potential +problems.") + (license license:gpl3))) + (define-public r-amaretto (package (name "r-amaretto") @@ -2287,13 +2334,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6")))) + "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -2337,6 +2384,65 @@ Methodologies included in the @code{ANCOMBC} package were designed to correct these biases and construct statistically consistent estimators.") (license license:artistic2.0))) +(define-public r-animalcules + (package + (name "r-animalcules") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "animalcules" version)) + (sha256 + (base32 + "1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr")))) + (properties `((upstream-name . "animalcules"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-assertthat + r-biomformat + r-caret + r-covr + r-deseq2 + r-dplyr + r-dt + r-forcats + r-ggplot2 + r-glmnet + r-gunifrac + r-lattice + r-limma + r-magrittr + r-matrix + r-multiassayexperiment + r-plotly + r-plotroc + r-rentrez + r-reshape2 + r-s4vectors + r-scales + r-shiny + r-shinyjs + r-summarizedexperiment + r-tibble + r-tsne + r-umap + r-vegan + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/compbiomed/animalcules") + (synopsis "Interactive microbiome analysis toolkit") + (description + "Animalcules is an R package for utilizing up-to-date data analytics, +visualization methods, and machine learning models to provide users an +easy-to-use interactive microbiome analysis framework. It can be used as a +standalone software package or users can explore their data with the +accompanying interactive R Shiny application. Traditional microbiome analysis +such as alpha/beta diversity and differential abundance analysis are enhanced, +while new methods like biomarker identification are introduced by animalcules. +Powerful interactive and dynamic figures generated by animalcules enable users +to understand their data better and discover new insights.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") @@ -2492,6 +2598,37 @@ mapped reads). It is currently designed for un-stranded paired-end RNA-seq data.") (license license:gpl2+))) +(define-public r-altcdfenvs + (package + (name "r-altcdfenvs") + (version "2.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "altcdfenvs" version)) + (sha256 + (base32 + "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0")))) + (properties `((upstream-name . "altcdfenvs"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-biostrings + r-hypergraph + r-makecdfenv + r-s4vectors)) + (home-page "https://bioconductor.org/packages/altcdfenvs") + (synopsis + "Convenience data structures and functions to handle CDF environments") + (description + "The package is usable with Affymetrix GeneChip short oligonucleotide +arrays, and it can be adapted or extended to other platforms. It is able to +modify or replace the grouping of probes in the probe sets. Also, the package +contains simple functions to read R connections in the FASTA format and it can +create an alternative mapping from sequences.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") @@ -2720,6 +2857,40 @@ biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables.") (license license:gpl3))) +(define-public r-asics + (package + (name "r-asics") + (version "2.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASICS" version)) + (sha256 + (base32 + "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7")))) + (properties `((upstream-name . "ASICS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-ggplot2 + r-glmnet + r-gridextra + r-matrix + r-mvtnorm + r-pepsnmr + r-plyr + r-quadprog + r-ropls + r-summarizedexperiment + r-zoo)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASICS") + (synopsis "Automatic statistical identification in complex spectra") + (description + "ASICS quantifies concentration of metabolites in a complex spectrum. +The identification of metabolites is performed by fitting a mixture model to +the spectra of the library with a sparse penalty.") + (license license:gpl2+))) + (define-public r-aspli (package (name "r-aspli") @@ -3121,13 +3292,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.0.2") + (version "3.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx")))) + "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -3164,13 +3335,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8")))) + "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -3309,6 +3480,44 @@ of Bioconductor.") packages.") (license license:artistic2.0))) +(define-public r-cardelino + (package + (name "r-cardelino") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "cardelino" version)) + (sha256 + (base32 + "1ma4clkrkrjvy12ln2d2smyzzsz9y9554f5wgwmh9kv6s4xc66qs")))) + (properties `((upstream-name . "cardelino"))) + (build-system r-build-system) + (propagated-inputs (list r-combinat + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggtree + r-matrix + r-matrixstats + r-pheatmap + r-s4vectors + r-snpstats + r-variantannotation + r-vcfr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/single-cell-genetics/cardelino") + (synopsis "Clone identification from single cell data") + (description + "This package provides methods to infer clonal tree configuration for a +population of cells using single-cell RNA-seq data (scRNA-seq), and possibly +other data modalities. Methods are also provided to assign cells to inferred +clones and explore differences in gene expression between clones. These +methods can flexibly integrate information from imperfect clonal trees +inferred based on bulk exome-seq data, and sparse variant alleles expressed in +scRNA-seq data. A flexible beta-binomial error model that accounts for +stochastic dropout events as well as systematic allelic imbalance is used.") + (license license:gpl3))) + (define-public r-coverageview (package (name "r-coverageview") @@ -3391,13 +3600,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg")))) + "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs @@ -3705,13 +3914,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l")))) + "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -3727,6 +3936,7 @@ negative control samples.") r-mass r-matrixstats r-methylkit + r-minfi r-nnls r-quadprog r-rsq @@ -4787,13 +4997,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.3") + (version "1.32.4") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0z2g3p6ip4g865na9bmqaa7w2s52769pmjr3hpiv6x8bhifh3nm5")))) + "1m4i27zx3ajwygwp38lrxf36rs575dkaxxc6jawpj1kzn7whi5ym")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -5154,26 +5364,26 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.38.1") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk")))) + "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel - r-genefilter r-geneplotter r-genomicranges r-ggplot2 r-iranges r-locfit + r-matrixstats r-rcpp r-rcpparmadillo r-s4vectors @@ -5386,13 +5596,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.40.0") + (version "3.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg")))) + "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -5511,14 +5721,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.80.0") + (version "1.80.2") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7")))) + "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5601,13 +5811,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.3") + (version "1.34.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv")))) + "1nskqmlar85zg96c1fbacl7dqg6r0gl814rc7yh482y4wgmwyg0r")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -5661,13 +5871,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.50.2") + (version "1.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz")))) + "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -5739,13 +5949,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.50.1") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966")))) + "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -5823,6 +6033,33 @@ testing and other simple calculations.") Enrichment Analysis} (GSEA).") (license license:artistic2.0))) +(define-public r-harshlight + (package + (name "r-harshlight") + (version "1.70.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Harshlight" version)) + (sha256 + (base32 + "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm")))) + (properties `((upstream-name . "Harshlight"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-altcdfenvs + r-biobase)) + (home-page "http://asterion.rockefeller.edu/Harshlight/") + (synopsis "Corrective make-up program for microarray chips") + (description + "The package detects extended diffuse and compact blemishes on microarray +chips. Harshlight marks the areas in a collection of chips (affybatch +objects). A corrected @code{AffyBatch} object will result. The package +replaces the defected areas with @code{N/A}s or the median of the values of +the same probe. The new version handles the substitute value as a whole +matrix to solve the memory problem.") + (license license:gpl2+))) + (define-public r-hpar (package (name "r-hpar") @@ -5875,13 +6112,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.72.1") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192")))) + "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -5944,13 +6181,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1")))) + (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) @@ -6010,6 +6247,33 @@ reduction (between group analysis) and joint dimension reduction of two datasets (coinertia analysis).") (license license:artistic2.0))) +(define-public r-makecdfenv + (package + (name "r-makecdfenv") + (version "1.74.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "makecdfenv" version)) + (sha256 + (base32 + "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25")))) + (properties `((upstream-name . "makecdfenv"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-affyio + r-biobase + r-zlibbioc)) + (home-page "https://bioconductor.org/packages/makecdfenv") + (synopsis "Chip description file environment maker") + (description + "This package implements two functions. One of them reads an Affymetrix +@acronym{CDF, chip description file} and creates a hash table environment +containing the location/probe set membership mapping. The other one creates a +package that automatically loads that environment.") + (license license:gpl2+))) + (define-public r-metaneighbor (package (name "r-metaneighbor") @@ -7050,13 +7314,13 @@ comprehensive scDblFinder method.") (define-public r-scmap (package (name "r-scmap") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm")))) + (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -7597,13 +7861,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng")))) + "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7970,14 +8234,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.62.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2")))) + "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -8115,14 +8379,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.8.1") + (version "3.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj")))) + "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -8323,6 +8587,35 @@ classification and ranking tasks. @dfn{Area under curve} (AUC), precision at a given recall, F-score for single and multiple classes are available.") (license license:gpl2+))) +(define-public r-pepsnmr + (package + (name "r-pepsnmr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "PepsNMR" version)) + (sha256 + (base32 + "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5")))) + (properties `((upstream-name . "PepsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-gridextra + r-matrix + r-matrixstats + r-ptw + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ManonMartin/PepsNMR") + (synopsis "Pre-process 1H-NMR FID signals") + (description + "This package provides R functions for common pre-processing steps that +are applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data. It +also provides a function to read the @acronym{FID, free induction decay} +signals directly in the Bruker format.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package @@ -8804,13 +9097,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "12jbqigg4k2ngrk2anbrrxrwkp57bbzdz492lg8lc6w1gygp5yip")))) + "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -9331,14 +9624,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.72.0") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld")))) + "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -9489,14 +9782,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.26.0") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi")))) + "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3")))) (build-system r-build-system) (arguments (list @@ -10378,14 +10671,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.22.0") + (version "2.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0")))) + "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -10726,14 +11019,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag")))) + "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -10848,14 +11141,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.18.1") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr")))) + "0nzcr23m58z3h0n0frxf26z14j7ilcl4fjy7rqm7f2i1wyld70zl")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -10926,13 +11219,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a")))) + "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -11695,14 +11988,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh")))) + "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -11711,6 +12004,7 @@ investigation using RNA-seq data.") r-delayedarray r-delayedmatrixstats r-gseabase + r-matrix r-mixtools r-r-utils r-shiny @@ -12531,14 +12825,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.34.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2")))) + "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -12971,14 +13265,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.12.0") + (version "2.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n")))) + "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -13204,14 +13498,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.26.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w")))) + "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -13427,38 +13721,30 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m")))) + "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-bh + r-biobase r-biocgenerics - r-clue + r-cpp11 r-data-table r-flowclust r-flowcore - r-flowstats r-flowviz r-flowworkspace r-graph - r-gtools - r-ks - r-lattice - r-mass r-ncdfflow - r-plyr - r-r-utils r-rbgl - r-rcolorbrewer - r-rcpp - r-rrcov)) + r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") @@ -13658,14 +13944,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.17.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk")))) + "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -15328,13 +15614,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23")))) + "1xplkzm29v6aysfhb6kf2nnmvc37jmcvv6vsgbx8z8qccn96jk02")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -15346,6 +15632,7 @@ functionality.") r-rcurl r-xml r-runit)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -15914,14 +16201,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.60.0") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda")))) + "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -15935,13 +16222,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.36.0") + (version "0.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs")))) + "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -16425,13 +16712,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp")))) + (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -16532,14 +16819,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.1") + (version "1.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2")))) + "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -16612,14 +16899,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih")))) + "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -17214,13 +17501,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.58.0") + (version "1.58.3") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq")))) + (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs |