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gnu: Add r-bionero.

* gnu/packages/bioconductor.scm (r-bionero): New variable.
master
Ricardo Wurmus 2021-09-07 14:38:08 +02:00
parent 2794024dc2
commit 4f6b3821eb
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@ -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")