diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 1754 |
1 files changed, 1752 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 710b9fd07a..deb179c4d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -29,7 +29,11 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) + #:use-module (gnu packages haskell) + #:use-module (gnu packages image) #:use-module (gnu packages maths) + #:use-module (gnu packages netpbm) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) @@ -708,9 +712,96 @@ annotations.") "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +(define-public r-do-db + (package + (name "r-do-db") + (version "2.9") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "DO.db_" version ".tar.gz")) + (sha256 + (base32 + "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) + (properties + `((upstream-name . "DO.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://www.bioconductor.org/packages/DO.db/") + (synopsis "Annotation maps describing the entire Disease Ontology") + (description + "This package provides a set of annotation maps describing the entire +Disease Ontology.") + (license license:artistic2.0))) + ;;; Experiment data +(define-public r-abadata + (package + (name "r-abadata") + (version "1.12.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "ABAData_" version ".tar.gz")) + (sha256 + (base32 + "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) + (properties + `((upstream-name . "ABAData"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://www.bioconductor.org/packages/ABAData/") + (synopsis "Gene expression in human brain regions from Allen Brain Atlas") + (description + "This package provides the data for the gene expression enrichment +analysis conducted in the package ABAEnrichment. The package includes three +datasets which are derived from the Allen Brain Atlas: + +@enumerate +@item Gene expression data from Human Brain (adults) averaged across donors, +@item Gene expression data from the Developing Human Brain pooled into five + age categories and averaged across donors, and +@item a developmental effect score based on the Developing Human Brain + expression data. +@end enumerate + +All datasets are restricted to protein coding genes.") + (license license:gpl2+))) + +(define-public r-arrmdata + (package + (name "r-arrmdata") + (version "1.18.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "ARRmData_" version ".tar.gz")) + (sha256 + (base32 + "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) + (properties + `((upstream-name . "ARRmData"))) + (build-system r-build-system) + (home-page "https://www.bioconductor.org/packages/ARRmData/") + (synopsis "Example dataset for normalization of Illumina 450k methylation data") + (description + "This package provides raw beta values from 36 samples across 3 groups +from Illumina 450k methylation arrays.") + (license license:artistic2.0))) + (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") @@ -1530,14 +1621,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp")))) + "1ykkr15b4bc2carwppf9yxzpl2n6lqpc6z6i2qy37vc6xffzgdx4")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -2521,3 +2612,1662 @@ summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.") (license license:expat))) + +;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-gkmsvm + (package + (name "r-gkmsvm") + (version "0.79.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gkmSVM" version)) + (sha256 + (base32 + "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) + (properties `((upstream-name . "gkmSVM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-kernlab" ,r-kernlab) + ("r-rcpp" ,r-rcpp) + ("r-rocr" ,r-rocr) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr))) + (home-page "https://cran.r-project.org/web/packages/gkmSVM") + (synopsis "Gapped-kmer support vector machine") + (description + "This R package provides tools for training gapped-kmer SVM classifiers +for DNA and protein sequences. This package supports several sequence +kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") + (license license:gpl2+))) + +(define-public r-triform + (package + (name "r-triform") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "triform" version)) + (sha256 + (base32 + "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-yaml" ,r-yaml))) + (home-page "https://bioconductor.org/packages/triform/") + (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") + (description + "The Triform algorithm uses model-free statistics to identify peak-like +distributions of TF ChIP sequencing reads, taking advantage of an improved +peak definition in combination with known profile characteristics.") + (license license:gpl2))) + +(define-public r-varianttools + (package + (name "r-varianttools") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "VariantTools" version)) + (sha256 + (base32 + "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j")))) + (properties `((upstream-name . "VariantTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/VariantTools/") + (synopsis "Tools for exploratory analysis of variant calls") + (description + "Explore, diagnose, and compare variant calls using filters. The +VariantTools package supports a workflow for loading data, calling single +sample variants and tumor-specific somatic mutations or other sample-specific +variant types (e.g., RNA editing). Most of the functions operate on +alignments (BAM files) or datasets of called variants. The user is expected +to have already aligned the reads with a separate tool, e.g., GSNAP via +gmapR.") + (license license:artistic2.0))) + +(define-public r-heatplus + (package + (name "r-heatplus") + (version "2.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Heatplus" version)) + (sha256 + (base32 + "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48")))) + (properties `((upstream-name . "Heatplus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://github.com/alexploner/Heatplus") + (synopsis "Heatmaps with row and/or column covariates and colored clusters") + (description + "This package provides tools to display a rectangular heatmap (intensity +plot) of a data matrix. By default, both samples (columns) and features (row) +of the matrix are sorted according to a hierarchical clustering, and the +corresponding dendrogram is plotted. Optionally, panels with additional +information about samples and features can be added to the plot.") + (license license:gpl2+))) + +(define-public r-gosemsim + (package + (name "r-gosemsim") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOSemSim" version)) + (sha256 + (base32 + "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib")))) + (properties `((upstream-name . "GOSemSim"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) + ("r-rcpp" ,r-rcpp))) + (home-page "https://guangchuangyu.github.io/software/GOSemSim") + (synopsis "GO-terms semantic similarity measures") + (description + "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide +quantitative ways to compute similarities between genes and gene groups, and +have became important basis for many bioinformatics analysis approaches. +GOSemSim is an R package for semantic similarity computation among GO terms, +sets of GO terms, gene products and gene clusters.") + (license license:artistic2.0))) + +(define-public r-anota + (package + (name "r-anota") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "anota" version)) + (sha256 + (base32 + "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-multtest" ,r-multtest) + ("r-qvalue" ,r-qvalue))) + (home-page "https://bioconductor.org/packages/anota/") + (synopsis "Analysis of translational activity") + (description + "Genome wide studies of translational control is emerging as a tool to +study verious biological conditions. The output from such analysis is both +the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively +involved in translation (the actively translating mRNA level) for each mRNA. +The standard analysis of such data strives towards identifying differential +translational between two or more sample classes - i.e. differences in +actively translated mRNA levels that are independent of underlying differences +in cytosolic mRNA levels. This package allows for such analysis using partial +variances and the random variance model. As 10s of thousands of mRNAs are +analyzed in parallell the library performs a number of tests to assure that +the data set is suitable for such analysis.") + (license license:gpl3))) + +(define-public r-sigpathway + (package + (name "r-sigpathway") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sigPathway" version)) + (sha256 + (base32 + "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3")))) + (properties `((upstream-name . "sigPathway"))) + (build-system r-build-system) + (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") + (synopsis "Pathway analysis") + (description + "This package is used to conduct pathway analysis by calculating the NT_k +and NE_k statistics in a statistical framework for determining whether a +specified group of genes for a pathway has a coordinated association with a +phenotype of interest.") + (license license:gpl2))) + +(define-public r-fgsea + (package + (name "r-fgsea") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fgsea" version)) + (sha256 + (base32 + "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-data-table" ,r-data-table) + ("r-fastmatch" ,r-fastmatch) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/ctlab/fgsea/") + (synopsis "Fast gene set enrichment analysis") + (description + "The package implements an algorithm for fast gene set enrichment +analysis. Using the fast algorithm allows to make more permutations and get +more fine grained p-values, which allows to use accurate stantard approaches +to multiple hypothesis correction.") + (license license:expat))) + +(define-public r-dose + (package + (name "r-dose") + (version "3.8.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DOSE" version)) + (sha256 + (base32 + "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa")))) + (properties `((upstream-name . "DOSE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocparallel" ,r-biocparallel) + ("r-do-db" ,r-do-db) + ("r-fgsea" ,r-fgsea) + ("r-ggplot2" ,r-ggplot2) + ("r-gosemsim" ,r-gosemsim) + ("r-qvalue" ,r-qvalue) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://guangchuangyu.github.io/software/DOSE/") + (synopsis "Disease ontology semantic and enrichment analysis") + (description + "This package implements five methods proposed by Resnik, Schlicker, +Jiang, Lin and Wang, respectively, for measuring semantic similarities among +@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses +including hypergeometric model and gene set enrichment analysis are also +implemented for discovering disease associations of high-throughput biological +data.") + (license license:artistic2.0))) + +(define-public r-enrichplot + (package + (name "r-enrichplot") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "enrichplot" version)) + (sha256 + (base32 + "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-cowplot" ,r-cowplot) + ("r-dose" ,r-dose) + ("r-europepmc" ,r-europepmc) + ("r-ggplot2" ,r-ggplot2) + ("r-ggplotify" ,r-ggplotify) + ("r-ggraph" ,r-ggraph) + ("r-ggridges" ,r-ggridges) + ("r-gosemsim" ,r-gosemsim) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-upsetr" ,r-upsetr))) + (home-page "https://github.com/GuangchuangYu/enrichplot") + (synopsis "Visualization of functional enrichment result") + (description + "The enrichplot package implements several visualization methods for +interpreting functional enrichment results obtained from ORA or GSEA analyses. +All the visualization methods are developed based on ggplot2 graphics.") + (license license:artistic2.0))) + +(define-public r-clusterprofiler + (package + (name "r-clusterprofiler") + (version "3.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "clusterProfiler" version)) + (sha256 + (base32 + "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm")))) + (properties + `((upstream-name . "clusterProfiler"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dose" ,r-dose) + ("r-enrichplot" ,r-enrichplot) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-gosemsim" ,r-gosemsim) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-qvalue" ,r-qvalue) + ("r-rvcheck" ,r-rvcheck) + ("r-tidyr" ,r-tidyr))) + (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") + (synopsis "Analysis and visualization of functional profiles for gene clusters") + (description + "This package implements methods to analyze and visualize functional +profiles (GO and KEGG) of gene and gene clusters.") + (license license:artistic2.0))) + +(define-public r-mlinterfaces + (package + (name "r-mlinterfaces") + (version "1.62.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MLInterfaces" version)) + (sha256 + (base32 + "1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp")))) + (properties `((upstream-name . "MLInterfaces"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cluster" ,r-cluster) + ("r-fpc" ,r-fpc) + ("r-gbm" ,r-gbm) + ("r-gdata" ,r-gdata) + ("r-genefilter" ,r-genefilter) + ("r-ggvis" ,r-ggvis) + ("r-hwriter" ,r-hwriter) + ("r-mass" ,r-mass) + ("r-mlbench" ,r-mlbench) + ("r-pls" ,r-pls) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rda" ,r-rda) + ("r-rpart" ,r-rpart) + ("r-sfsmisc" ,r-sfsmisc) + ("r-shiny" ,r-shiny) + ("r-threejs" ,r-threejs))) + (home-page "https://bioconductor.org/packages/MLInterfaces/") + (synopsis "Interfaces to R machine learning procedures") + (description + "This package provides uniform interfaces to machine learning code for +data in R and Bioconductor containers.") + ;; Any version of the LGPL. + (license license:lgpl2.1+))) + +(define-public r-annaffy + (package + (name "r-annaffy") + (version "1.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "annaffy" version)) + (sha256 + (base32 + "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-reference-to-non-free-data + (lambda _ + (substitute* "DESCRIPTION" + ((", KEGG.db") "")) + #t))))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-dbi" ,r-dbi) + ("r-go-db" ,r-go-db))) + (home-page "https://bioconductor.org/packages/annaffy/") + (synopsis "Annotation tools for Affymetrix biological metadata") + (description + "This package provides functions for handling data from Bioconductor +Affymetrix annotation data packages. It produces compact HTML and text +reports including experimental data and URL links to many online databases. +It allows searching of biological metadata using various criteria.") + ;; Any version of the LGPL according to the DESCRIPTION file. A copy of + ;; the LGPL 2.1 is included. + (license license:lgpl2.1+))) + +(define-public r-a4core + (package + (name "r-a4core") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Core" version)) + (sha256 + (base32 + "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr")))) + (properties `((upstream-name . "a4Core"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-glmnet" ,r-glmnet))) + (home-page "https://bioconductor.org/packages/a4Core") + (synopsis "Automated Affymetrix array analysis core package") + (description + "This is the core package for the automated analysis of Affymetrix +arrays.") + (license license:gpl3))) + +(define-public r-a4classif + (package + (name "r-a4classif") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Classif" version)) + (sha256 + (base32 + "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j")))) + (properties `((upstream-name . "a4Classif"))) + (build-system r-build-system) + (propagated-inputs + `(("r-a4core" ,r-a4core) + ("r-a4preproc" ,r-a4preproc) + ("r-glmnet" ,r-glmnet) + ("r-mlinterfaces" ,r-mlinterfaces) + ("r-pamr" ,r-pamr) + ("r-rocr" ,r-rocr) + ("r-varselrf" ,r-varselrf))) + (home-page "https://bioconductor.org/packages/a4Classif/") + (synopsis "Automated Affymetrix array analysis classification package") + (description + "This is the classification package for the automated analysis of +Affymetrix arrays.") + (license license:gpl3))) + +(define-public r-a4preproc + (package + (name "r-a4preproc") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Preproc" version)) + (sha256 + (base32 + "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp")))) + (properties `((upstream-name . "a4Preproc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/a4Preproc/") + (synopsis "Automated Affymetrix array analysis preprocessing package") + (description + "This is a package for the automated analysis of Affymetrix arrays. It +is used for preprocessing the arrays.") + (license license:gpl3))) + +(define-public r-a4reporting + (package + (name "r-a4reporting") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Reporting" version)) + (sha256 + (base32 + "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4")))) + (properties `((upstream-name . "a4Reporting"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annaffy" ,r-annaffy) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/a4Reporting/") + (synopsis "Automated Affymetrix array analysis reporting package") + (description + "This is a package for the automated analysis of Affymetrix arrays. It +provides reporting features.") + (license license:gpl3))) + +(define-public r-a4base + (package + (name "r-a4base") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Base" version)) + (sha256 + (base32 + "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70")))) + (properties `((upstream-name . 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AbseqR empowers the users of abseqPy with plotting and reporting +capabilities and allows them to generate interactive HTML reports for the +convenience of viewing and sharing with other researchers. Additionally, +abseqR extends abseqPy to compare multiple repertoire analyses and perform +further downstream analysis on its output.") + (license license:gpl3))) + +(define-public r-bacon + (package + (name "r-bacon") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bacon" version)) + (sha256 + (base32 + "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-ellipse" ,r-ellipse) + ("r-ggplot2" ,r-ggplot2))) + (home-page "https://bioconductor.org/packages/bacon/") + (synopsis "Controlling bias and inflation in association studies") + (description + "Bacon can be used to remove inflation and bias often observed in +epigenome- and transcriptome-wide association studies. To this end bacon +constructs an empirical null distribution using a Gibbs Sampling algorithm by +fitting a three-component normal mixture on z-scores.") + (license license:gpl2+))) + +(define-public r-rgadem + (package + (name "r-rgadem") + (version "2.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rGADEM" version)) + (sha256 + (base32 + "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2")))) + (properties `((upstream-name . "rGADEM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-iranges" ,r-iranges) + ("r-seqlogo" ,r-seqlogo))) + (home-page "https://bioconductor.org/packages/rGADEM/") + (synopsis "De novo sequence motif discovery") + (description + "rGADEM is an efficient de novo motif discovery tool for large-scale +genomic sequence data.") + (license license:artistic2.0))) + +(define-public r-motiv + (package + (name "r-motiv") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MotIV" version)) + (sha256 + (base32 + "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8")))) + (properties `((upstream-name . "MotIV"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-rgadem" ,r-rgadem) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/MotIV/") + (synopsis "Motif identification and validation") + (description + "This package is used for the identification and validation of sequence +motifs. It makes use of STAMP for comparing a set of motifs to a given +database (e.g. JASPAR). It can also be used to visualize motifs, motif +distributions, modules and filter motifs.") + (license license:gpl2))) + +(define-public r-motifstack + (package + (name "r-motifstack") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifStack" version)) + (sha256 + (base32 + "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf")))) + (properties `((upstream-name . "motifStack"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-biostrings" ,r-biostrings) + ("r-grimport" ,r-grimport) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-motiv" ,r-motiv) + ("r-scales" ,r-scales) + ("r-xml" ,r-xml))) + (home-page "https://bioconductor.org/packages/motifStack/") + (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") + (description + "The motifStack package is designed for graphic representation of +multiple motifs with different similarity scores. It works with both DNA/RNA +sequence motifs and amino acid sequence motifs. In addition, it provides the +flexibility for users to customize the graphic parameters such as the font +type and symbol colors.") + (license license:gpl2+))) + +(define-public r-genomicscores + (package + (name "r-genomicscores") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicScores" version)) + (sha256 + (base32 + "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n")))) + (properties `((upstream-name . "GenomicScores"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml))) + (home-page "https://github.com/rcastelo/GenomicScores/") + (synopsis "Work with genome-wide position-specific scores") + (description + "This package provides infrastructure to store and access genome-wide +position-specific scores within R and Bioconductor.") + (license license:artistic2.0))) + +(define-public r-atacseqqc + (package + (name "r-atacseqqc") + (version "1.6.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ATACseqQC" version)) + (sha256 + (base32 + "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn")))) + (properties `((upstream-name . "ATACseqQC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-chippeakanno" ,r-chippeakanno) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-genomicscores" ,r-genomicscores) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-limma" ,r-limma) + ("r-motifstack" ,r-motifstack) + ("r-preseqr" ,r-preseqr) + ("r-randomforest" ,r-randomforest) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/ATACseqQC/") + (synopsis "ATAC-seq quality control") + (description + "ATAC-seq, an assay for Transposase-Accessible Chromatin using +sequencing, is a rapid and sensitive method for chromatin accessibility +analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq +and DNAse-seq. The ATACseqQC package was developed to help users to quickly +assess whether their ATAC-seq experiment is successful. It includes +diagnostic plots of fragment size distribution, proportion of mitochondria +reads, nucleosome positioning pattern, and CTCF or other Transcript Factor +footprints.") + (license license:gpl2+))) + +(define-public r-gofuncr + (package + (name "r-gofuncr") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOfuncR" version)) + (sha256 + (base32 + "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk")))) + (properties `((upstream-name . "GOfuncR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-mapplots" ,r-mapplots) + ("r-rcpp" ,r-rcpp) + ("r-vioplot" ,r-vioplot))) + (home-page "https://bioconductor.org/packages/GOfuncR/") + (synopsis "Gene ontology enrichment using FUNC") + (description + "GOfuncR performs a gene ontology enrichment analysis based on the +ontology enrichment software FUNC. GO-annotations are obtained from +OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is +included in the package and updated regularly. GOfuncR provides the standard +candidate vs background enrichment analysis using the hypergeometric test, as +well as three additional tests: + +@enumerate +@item the Wilcoxon rank-sum test that is used when genes are ranked, +@item a binomial test that is used when genes are associated with two counts, + and +@item a Chi-square or Fisher's exact test that is used in cases when genes are +associated with four counts. +@end enumerate + +To correct for multiple testing and interdependency of the tests, family-wise +error rates are computed based on random permutations of the gene-associated +variables. GOfuncR also provides tools for exploring the ontology graph and +the annotations, and options to take gene-length or spatial clustering of +genes into account. It is also possible to provide custom gene coordinates, +annotations and ontologies.") + (license license:gpl2+))) + +(define-public r-abaenrichment + (package + (name "r-abaenrichment") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ABAEnrichment" version)) + (sha256 + (base32 + "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v")))) + (properties `((upstream-name . "ABAEnrichment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abadata" ,r-abadata) + ("r-data-table" ,r-data-table) + ("r-gofuncr" ,r-gofuncr) + ("r-gplots" ,r-gplots) + ("r-gtools" ,r-gtools) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/ABAEnrichment/") + (synopsis "Gene expression enrichment in human brain regions") + (description + "The package ABAEnrichment is designed to test for enrichment of user +defined candidate genes in the set of expressed genes in different human brain +regions. The core function @code{aba_enrich} integrates the expression of the +candidate gene set (averaged across donors) and the structural information of +the brain using an ontology, both provided by the Allen Brain Atlas project.") + (license license:gpl2+))) + +(define-public r-annotationfuncs + (package + (name "r-annotationfuncs") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationFuncs" version)) + (sha256 + (base32 + "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss")))) + (properties + `((upstream-name . "AnnotationFuncs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dbi" ,r-dbi))) + (home-page "https://www.iysik.com/r/annotationfuncs") + (synopsis "Annotation translation functions") + (description + "This package provides functions for handling translating between +different identifieres using the Biocore Data Team data-packages (e.g. +@code{org.Bt.eg.db}).") + (license license:gpl2))) + +(define-public r-annotationtools + (package + (name "r-annotationtools") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "annotationTools" version)) + (sha256 + (base32 + "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z")))) + (properties + `((upstream-name . "annotationTools"))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/annotationTools/") + (synopsis "Annotate microarrays and perform gene expression analyses") + (description + "This package provides functions to annotate microarrays, find orthologs, +and integrate heterogeneous gene expression profiles using annotation and +other molecular biology information available as flat file database (plain +text files).") + ;; Any version of the GPL. + (license (list license:gpl2+)))) + +(define-public r-allelicimbalance + (package + (name "r-allelicimbalance") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AllelicImbalance" version)) + (sha256 + (base32 + "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91")))) + (properties + `((upstream-name . "AllelicImbalance"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-gridextra" ,r-gridextra) + ("r-gviz" ,r-gviz) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-nlme" ,r-nlme) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://github.com/pappewaio/AllelicImbalance") + (synopsis "Investigate allele-specific expression") + (description + "This package provides a framework for allele-specific expression +investigation using RNA-seq data.") + (license license:gpl3))) + +(define-public r-aucell + (package + (name "r-aucell") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AUCell" version)) + (sha256 + (base32 + "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9")))) + (properties `((upstream-name . "AUCell"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-gseabase" ,r-gseabase) + ("r-mixtools" ,r-mixtools) + ("r-r-utils" ,r-r-utils) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/AUCell/") + (synopsis "Analysis of gene set activity in single-cell RNA-seq data") + (description + "AUCell allows to identify cells with active gene sets (e.g. signatures, +gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area +Under the Curve} (AUC) to calculate whether a critical subset of the input +gene set is enriched within the expressed genes for each cell. The +distribution of AUC scores across all the cells allows exploring the relative +expression of the signature. Since the scoring method is ranking-based, +AUCell is independent of the gene expression units and the normalization +procedure. In addition, since the cells are evaluated individually, it can +easily be applied to bigger datasets, subsetting the expression matrix if +needed.") + (license license:gpl3))) + +(define-public r-ebimage + (package + (name "r-ebimage") + (version "4.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EBImage" version)) + (sha256 + (base32 + "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx")))) + (properties `((upstream-name . "EBImage"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fftwtools" ,r-fftwtools) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jpeg" ,r-jpeg) + ("r-locfit" ,r-locfit) + ("r-png" ,r-png) + ("r-rcurl" ,r-rcurl) + ("r-tiff" ,r-tiff))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/aoles/EBImage") + (synopsis "Image processing and analysis toolbox for R") + (description + "EBImage provides general purpose functionality for image processing and +analysis. In the context of (high-throughput) microscopy-based cellular +assays, EBImage offers tools to segment cells and extract quantitative +cellular descriptors. This allows the automation of such tasks using the R +programming language and facilitates the use of other tools in the R +environment for signal processing, statistical modeling, machine learning and +visualization with image data.") + ;; Any version of the LGPL. + (license license:lgpl2.1+))) + +(define-public r-yamss + (package + (name "r-yamss") + (version "1.8.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "yamss" version)) + (sha256 + (base32 + "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-ebimage" ,r-ebimage) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-mzr" ,r-mzr) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" + ,r-summarizedexperiment))) + (home-page "https://github.com/hansenlab/yamss") + (synopsis "Tools for high-throughput metabolomics") + (description + "This package provides tools to analyze and visualize high-throughput +metabolomics data acquired using chromatography-mass spectrometry. These tools +preprocess data in a way that enables reliable and powerful differential +analysis.") + (license license:artistic2.0))) + +(define-public r-gtrellis + (package + (name "r-gtrellis") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gtrellis" version)) + (sha256 + (base32 + "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-genomicranges" ,r-genomicranges) + ("r-getoptlong" ,r-getoptlong) + ("r-iranges" ,r-iranges))) + (home-page "https://github.com/jokergoo/gtrellis") + (synopsis "Genome level Trellis layout") + (description + "Genome level Trellis graph visualizes genomic data conditioned by +genomic categories (e.g. chromosomes). For each genomic category, multiple +dimensional data which are represented as tracks describe different features +from different aspects. This package provides high flexibility to arrange +genomic categories and to add self-defined graphics in the plot.") + (license license:expat))) + +(define-public r-somaticsignatures + (package + (name "r-somaticsignatures") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SomaticSignatures" version)) + (sha256 + (base32 + "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02")))) + (properties + `((upstream-name . "SomaticSignatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-nmf" ,r-nmf) + ("r-pcamethods" ,r-pcamethods) + ("r-proxy" ,r-proxy) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://github.com/juliangehring/SomaticSignatures") + (synopsis "Somatic signatures") + (description + "This package identifies mutational signatures of @dfn{single nucleotide +variants} (SNVs). It provides a infrastructure related to the methodology +described in Nik-Zainal (2012, Cell), with flexibility in the matrix +decomposition algorithms.") + (license license:expat))) + +(define-public r-yapsa + (package + (name "r-yapsa") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "YAPSA" version)) + (sha256 + (base32 + "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j")))) + (properties `((upstream-name . "YAPSA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-complexheatmap" ,r-complexheatmap) + ("r-corrplot" ,r-corrplot) + ("r-dendextend" ,r-dendextend) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-getoptlong" ,r-getoptlong) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtrellis" ,r-gtrellis) + ("r-keggrest" ,r-keggrest) + ("r-lsei" ,r-lsei) + ("r-pmcmr" ,r-pmcmr) + ("r-reshape2" ,r-reshape2) + ("r-somaticsignatures" ,r-somaticsignatures) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/YAPSA/") + (synopsis "Yet another package for signature analysis") + (description + "This package provides functions and routines useful in the analysis of +somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, +functions to perform a signature analysis with known signatures and a +signature analysis on @dfn{stratified mutational catalogue} (SMC) are +provided.") + (license license:gpl3))) + +(define-public r-gcrma + (package + (name "r-gcrma") + (version "2.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gcrma" version)) + (sha256 + (base32 + "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-biostrings" ,r-biostrings) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/gcrma/") + (synopsis "Background adjustment using sequence information") + (description + "Gcrma adjusts for background intensities in Affymetrix array data which +include optical noise and @dfn{non-specific binding} (NSB). The main function +@code{gcrma} converts background adjusted probe intensities to expression +measures using the same normalization and summarization methods as a +@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information +to estimate probe affinity to NSB. The sequence information is summarized in +a more complex way than the simple GC content. Instead, the base types (A, T, +G or C) at each position along the probe determine the affinity of each probe. +The parameters of the position-specific base contributions to the probe +affinity is estimated in an NSB experiment in which only NSB but no +gene-specific bidning is expected.") + ;; Any version of the LGPL + (license license:lgpl2.1+))) + +(define-public r-simpleaffy + (package + (name "r-simpleaffy") + (version "2.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "simpleaffy" version)) + (sha256 + (base32 + "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-gcrma" ,r-gcrma) + ("r-genefilter" ,r-genefilter))) + (home-page "https://bioconductor.org/packages/simpleaffy/") + (synopsis "Very simple high level analysis of Affymetrix data") + (description + "This package provides high level functions for reading Affy @file{.CEL} +files, phenotypic data, and then computing simple things with it, such as +t-tests, fold changes and the like. It makes heavy use of the @code{affy} +library. It also has some basic scatter plot functions and mechanisms for +generating high resolution journal figures.") + (license license:gpl2+))) + +(define-public r-yaqcaffy + (package + (name "r-yaqcaffy") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "yaqcaffy" version)) + (sha256 + (base32 + "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-simpleaffy" ,r-simpleaffy))) + (home-page "https://bioconductor.org/packages/yaqcaffy/") + (synopsis "Affymetrix quality control and reproducibility analysis") + (description + "This is a package that can be used for quality control of Affymetrix +GeneChip expression data and reproducibility analysis of human whole genome +chips with the MAQC reference datasets.") + (license license:artistic2.0))) + +(define-public r-quantro + (package + (name "r-quantro") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "quantro" version)) + (sha256 + (base32 + "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-minfi" ,r-minfi) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://bioconductor.org/packages/quantro/") + (synopsis "Test for when to use quantile normalization") + (description + "This package provides a data-driven test for the assumptions of quantile +normalization using raw data such as objects that inherit eSets (e.g. +ExpressionSet, MethylSet). Group level information about each sample (such as +Tumor / Normal status) must also be provided because the test assesses if +there are global differences in the distributions between the user-defined +groups.") + (license license:gpl3+))) + +(define-public r-yarn + (package + (name "r-yarn") + (version "1.8.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "yarn" version)) + (sha256 + (base32 + "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biomart" ,r-biomart) + ("r-downloader" ,r-downloader) + ("r-edger" ,r-edger) + ("r-gplots" ,r-gplots) + ("r-limma" ,r-limma) + ("r-matrixstats" ,r-matrixstats) + ("r-preprocesscore" ,r-preprocesscore) + ("r-quantro" ,r-quantro) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-readr" ,r-readr))) + (home-page "https://bioconductor.org/packages/yarn/") + (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") + (description + "Expedite large RNA-Seq analyses using a combination of previously +developed tools. YARN is meant to make it easier for the user in performing +basic mis-annotation quality control, filtering, and condition-aware +normalization. YARN leverages many Bioconductor tools and statistical +techniques to account for the large heterogeneity and sparsity found in very +large RNA-seq experiments.") + (license license:artistic2.0))) + +(define-public r-roar + (package + (name "r-roar") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "roar" version)) + (sha256 + (base32 + "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://github.com/vodkatad/roar/") + (synopsis "Identify differential APA usage from RNA-seq alignments") + (description + "This package provides tools for identifying preferential usage of APA +sites, comparing two biological conditions, starting from known alternative +sites and alignments obtained from standard RNA-seq experiments.") + (license license:gpl3))) + +(define-public r-xbseq + (package + (name "r-xbseq") + (version "1.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "XBSeq" version)) + (sha256 + (base32 + "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph")))) + (properties `((upstream-name . "XBSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-locfit" ,r-locfit) + ("r-magrittr" ,r-magrittr) + ("r-matrixstats" ,r-matrixstats) + ("r-pracma" ,r-pracma) + ("r-roar" ,r-roar))) + (home-page "https://github.com/Liuy12/XBSeq") + (synopsis "Test for differential expression for RNA-seq data") + (description + "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential +expression} (DE), where a statistical model was established based on the +assumption that observed signals are the convolution of true expression +signals and sequencing noises. The mapped reads in non-exonic regions are +considered as sequencing noises, which follows a Poisson distribution. Given +measurable observed signal and background noise from RNA-seq data, true +expression signals, assuming governed by the negative binomial distribution, +can be delineated and thus the accurate detection of differential expressed +genes.") + (license license:gpl3+))) + +(define-public r-massspecwavelet + (package + (name "r-massspecwavelet") + (version "1.48.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MassSpecWavelet" version)) + (sha256 + (base32 + "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz")))) + (properties + `((upstream-name . "MassSpecWavelet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-waveslim" ,r-waveslim))) + (home-page "https://bioconductor.org/packages/MassSpecWavelet/") + (synopsis "Mass spectrum processing by wavelet-based algorithms") + (description + "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) +data mainly through the use of wavelet transforms. It supports peak detection +based on @dfn{Continuous Wavelet Transform} (CWT).") + (license license:lgpl2.0+))) + +(define-public r-xcms + (package + (name "r-xcms") + (version "3.4.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "xcms" version)) + (sha256 + (base32 + "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-lattice" ,r-lattice) + ("r-massspecwavelet" ,r-massspecwavelet) + ("r-msnbase" ,r-msnbase) + ("r-multtest" ,r-multtest) + ("r-mzr" ,r-mzr) + ("r-plyr" ,r-plyr) + ("r-protgenerics" ,r-protgenerics) + ("r-rann" ,r-rann) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-robustbase" ,r-robustbase) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/xcms/") + (synopsis "LC/MS and GC/MS mass spectrometry data analysis") + (description + "This package provides a framework for processing and visualization of +chromatographically separated and single-spectra mass spectral data. It +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-wrench + (package + (name "r-wrench") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Wrench" version)) + (sha256 + (base32 + "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg")))) + (properties `((upstream-name . "Wrench"))) + (build-system r-build-system) + (propagated-inputs + `(("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-matrixstats" ,r-matrixstats))) + (home-page "https://github.com/HCBravoLab/Wrench") + (synopsis "Wrench normalization for sparse count data") + (description + "Wrench is a package for normalization sparse genomic count data, like +that arising from 16s metagenomic surveys.") + (license license:artistic2.0))) + +(define-public r-wiggleplotr + (package + (name "r-wiggleplotr") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "wiggleplotr" version)) + (sha256 + (base32 + "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-purrr" ,r-purrr) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/wiggleplotr/") + (synopsis "Make read coverage plots from BigWig files") + (description + "This package provides tools to visualize read coverage from sequencing +experiments together with genomic annotations (genes, transcripts, peaks). +Introns of long transcripts can be rescaled to a fixed length for better +visualization of exonic read coverage.") + (license license:asl2.0))) + +(define-public r-widgettools + (package + (name "r-widgettools") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "widgetTools" version)) + (sha256 + (base32 + "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf")))) + (properties `((upstream-name . "widgetTools"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/widgetTools/") + (synopsis "Tools for creating interactive tcltk widgets") + (description + "This packages contains tools to support the construction of tcltk +widgets in R.") + ;; Any version of the LGPL. + (license license:lgpl3+))) + +(define-public r-webbioc + (package + (name "r-webbioc") + (version "1.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "webbioc" version)) + (sha256 + (base32 + "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi")))) + (build-system r-build-system) + (inputs + `(("netpbm" ,netpbm) + ("perl" ,perl))) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-annaffy" ,r-annaffy) + ("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-gcrma" ,r-gcrma) + ("r-multtest" ,r-multtest) + ("r-qvalue" ,r-qvalue) + ("r-vsn" ,r-vsn))) + (home-page "https://www.bioconductor.org/") + (synopsis "Bioconductor web interface") + (description + "This package provides an integrated web interface for doing microarray +analysis using several of the Bioconductor packages. It is intended to be +deployed as a centralized bioinformatics resource for use by many users. +Currently only Affymetrix oligonucleotide analysis is supported.") + (license license:gpl2+))) + +(define-public r-zfpkm + (package + (name "r-zfpkm") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zFPKM" version)) + (sha256 + (base32 + "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5")))) + (properties `((upstream-name . "zFPKM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/ronammar/zFPKM/") + (synopsis "Functions to facilitate zFPKM transformations") + (description + "This is a package to perform the zFPKM transform on RNA-seq FPKM data. +This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID +24215113).") + (license license:gpl3))) + +(define-public r-rbowtie2 + (package + (name "r-rbowtie2") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rbowtie2" version)) + (sha256 + (base32 + "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr")))) + (properties `((upstream-name . "Rbowtie2"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (home-page "https://bioconductor.org/packages/Rbowtie2/") + (synopsis "R wrapper for Bowtie2 and AdapterRemoval") + (description + "This package provides an R wrapper of the popular @code{bowtie2} +sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for +rapid adapter trimming, identification, and read merging.") + (license license:gpl3+))) + +(define-public r-progeny + (package + (name "r-progeny") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "progeny" version)) + (sha256 + (base32 + "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7")))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://github.com/saezlab/progeny") + (synopsis "Pathway responsive gene activity inference") + (description + "This package provides a function to infer pathway activity from gene +expression. It contains the linear model inferred in the publication +\"Perturbation-response genes reveal signaling footprints in cancer gene +expression\".") + (license license:asl2.0))) + +(define-public r-arrmnormalization + (package + (name "r-arrmnormalization") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ARRmNormalization" version)) + (sha256 + (base32 + "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd")))) + (properties + `((upstream-name . "ARRmNormalization"))) + (build-system r-build-system) + (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) + (home-page "https://bioconductor.org/packages/ARRmNormalization/") + (synopsis "Adaptive robust regression normalization for methylation data") + (description + "This is a package to perform the @dfn{Adaptive Robust Regression +method} (ARRm) for the normalization of methylation data from the Illumina +Infinium HumanMethylation 450k assay.") + (license license:artistic2.0))) |