diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 221 |
1 files changed, 209 insertions, 12 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3810749f83..e87907fac5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -590,6 +590,35 @@ data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) +(define-public r-txdb-hsapiens-ucsc-hg38-knowngene + (package + (name "r-txdb-hsapiens-ucsc-hg38-knowngene") + (version "3.4.6") + (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://bioconductor.org/packages/" + "release/data/annotation/src/contrib" + "/TxDb.Hsapiens.UCSC.hg38.knownGene_" + version ".tar.gz")) + (sha256 + (base32 + "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) + (properties + `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures))) + (home-page + "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") + (synopsis "Annotation package for human genome in TxDb format") + (description + "This package provides an annotation database of Homo sapiens genome +data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" +track. The database is exposed as a @code{TxDb} object.") + (license license:artistic2.0))) + (define-public r-txdb-mmusculus-ucsc-mm9-knowngene (package (name "r-txdb-mmusculus-ucsc-mm9-knowngene") @@ -1153,14 +1182,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.18.0") + (version "3.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "089v16mm5m0rlyyyd0d6rz8gwb852zf3bcdrrw70wanlfjn258q7")))) + "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -2086,14 +2115,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc")))) + "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -2886,14 +2915,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.10.0") + (version "3.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv")))) + "0ab7mgj42fg6608qkciyqivr1n8s8r5ibvp0z3jfclrnyx6cl0w1")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -3408,14 +3437,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj")))) + "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -3621,14 +3650,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm")))) + "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -4438,14 +4467,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "01jhj5vvfl4n2d0nl3nd1iw9nii85mgw2adnrmxb8wwlxgy240vr")))) + "1y3zqvk1vbcb10r1myh6f5yzjvf7bhwhpiq78bs1k6spli4bzj0q")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (native-inputs @@ -4548,3 +4577,171 @@ high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.") (license license:gpl2+))) + +(define-public r-birewire + (package + (name "r-birewire") + (version "3.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiRewire" version)) + (sha256 + (base32 + "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) + (properties `((upstream-name . "BiRewire"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-slam" ,r-slam) + ("r-tsne" ,r-tsne))) + (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") + (synopsis "Tools for randomization of bipartite graphs") + (description + "This package provides functions for bipartite network rewiring through N +consecutive switching steps and for the computation of the minimal number of +switching steps to be performed in order to maximise the dissimilarity with +respect to the original network. It includes functions for the analysis of +the introduced randomness across the switching steps and several other +routines to analyse the resulting networks and their natural projections.") + (license license:gpl3))) + +(define-public r-birta + (package + (name "r-birta") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "birta" version)) + (sha256 + (base32 + "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limma" ,r-limma) + ("r-mass" ,r-mass))) + (home-page "https://bioconductor.org/packages/birta") + (synopsis "Bayesian inference of regulation of transcriptional activity") + (description + "Expression levels of mRNA molecules are regulated by different +processes, comprising inhibition or activation by transcription factors and +post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian +Inference of Regulation of Transcriptional Activity) uses the regulatory +networks of transcription factors and miRNAs together with mRNA and miRNA +expression data to predict switches in regulatory activity between two +conditions. A Bayesian network is used to model the regulatory structure and +Markov-Chain-Monte-Carlo is applied to sample the activity states.") + (license license:gpl2+))) + +(define-public r-ropls + (package + (name "r-ropls") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ropls" version)) + (sha256 + (base32 + "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2")))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") + (synopsis "Multivariate analysis and feature selection of omics data") + (description + "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) +and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, +regression, classification, and feature selection of omics data where the +number of variables exceeds the number of samples and with multicollinearity +among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to +separately model the variation correlated (predictive) to the factor of +interest and the uncorrelated (orthogonal) variation. While performing +similarly to PLS, OPLS facilitates interpretation. + +This package provides imlementations of PCA, PLS, and OPLS for multivariate +analysis and feature selection of omics data. In addition to scores, loadings +and weights plots, the package provides metrics and graphics to determine the +optimal number of components (e.g. with the R2 and Q2 coefficients), check the +validity of the model by permutation testing, detect outliers, and perform +feature selection (e.g. with Variable Importance in Projection or regression +coefficients).") + (license license:cecill))) + +(define-public r-biosigner + (package + (name "r-biosigner") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biosigner" version)) + (sha256 + (base32 + "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-e1071" ,r-e1071) + ("r-randomforest" ,r-randomforest) + ("r-ropls" ,r-ropls))) + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("pandoc" ,ghc-pandoc) + ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes + (home-page "https://bioconductor.org/packages/biosigner/") + (synopsis "Signature discovery from omics data") + (description + "Feature selection is critical in omics data analysis to extract +restricted and meaningful molecular signatures from complex and high-dimension +data, and to build robust classifiers. This package implements a method to +assess the relevance of the variables for the prediction performances of the +classifier. The approach can be run in parallel with the PLS-DA, Random +Forest, and SVM binary classifiers. The signatures and the corresponding +'restricted' models are returned, enabling future predictions on new +datasets.") + (license license:cecill))) + +(define-public r-annotatr + (package + (name "r-annotatr") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "annotatr" version)) + (sha256 + (base32 + "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-readr" ,r-readr) + ("r-regioner" ,r-regioner) + ("r-reshape2" ,r-reshape2) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/annotatr/") + (synopsis "Annotation of genomic regions to genomic annotations") + (description + "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, +differentially methylated CpGs or regions, SNPs, etc.) it is often of interest +to investigate the intersecting genomic annotations. Such annotations include +those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), +CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as +enhancers. The annotatr package provides an easy way to summarize and +visualize the intersection of genomic sites/regions with genomic +annotations.") + (license license:gpl3))) |