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-rw-r--r-- | gnu/packages/bioconductor.scm | 56 |
1 files changed, 56 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b6e7c877ff..8d7210d4ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14277,6 +14277,62 @@ throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.") (license license:gpl2+))) +(define-public r-bionero + (package + (name "r-bionero") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNERO" version)) + (sha256 + (base32 + "1yj0pavyfrj2gsvaj1dkgmznibm2appxjx9rk5qjslhslmm5b05b")))) + (properties `((upstream-name . "BioNERO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-complexheatmap" ,r-complexheatmap) + ("r-deseq2" ,r-deseq2) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-genie3" ,r-genie3) + ("r-ggnetwork" ,r-ggnetwork) + ("r-ggnewscale" ,r-ggnewscale) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-igraph" ,r-igraph) + ("r-intergraph" ,r-intergraph) + ("r-matrixstats" ,r-matrixstats) + ("r-minet" ,r-minet) + ("r-netrep" ,r-netrep) + ("r-networkd3" ,r-networkd3) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-sva" ,r-sva) + ("r-wgcna" ,r-wgcna))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/almeidasilvaf/BioNERO") + (synopsis "Biological network reconstruction omnibus") + (description + "BioNERO aims to integrate all aspects of biological network inference in +a single package, including data preprocessing, exploratory analyses, network +inference, and analyses for biological interpretations. BioNERO can be used +to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) +from gene expression data. Additionally, it can be used to explore +topological properties of protein-protein interaction (PPI) networks. GCN +inference relies on the popular WGCNA algorithm. GRN inference is based on +the \"wisdom of the crowds\" principle, which consists in inferring GRNs with +multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average +rank for each interaction pair. As all steps of network analyses are included +in this package, BioNERO makes users avoid having to learn the syntaxes of +several packages and how to communicate between them. Finally, users can also +identify consensus modules across independent expression sets and calculate +intra and interspecies module preservation statistics between different +networks.") + (license license:gpl3))) + (define-public r-tximeta (package (name "r-tximeta") |