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authorRicardo Wurmus <rekado@elephly.net>2021-09-07 14:38:08 +0200
committerRicardo Wurmus <rekado@elephly.net>2021-09-07 14:47:56 +0200
commit4f6b3821eb473f1fbd12beaa6ddf5a1474de6fa2 (patch)
treea9ea507fb674af9ae73c6107998e3126c6169216 /gnu/packages/bioconductor.scm
parent2794024dc276e6472137c33853bbef35eabac186 (diff)
gnu: Add r-bionero.
* gnu/packages/bioconductor.scm (r-bionero): New variable.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r--gnu/packages/bioconductor.scm56
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")