GWENA

DOI: 10.18129/B9.bioc.GWENA    

Pipeline for augmented co-expression analysis

Bioconductor version: Release (3.13)

The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.

Author: Gwenaëlle Lemoine [aut, cre] , Marie-Pier Scott-Boyer [ths], Arnaud Droit [fnd]

Maintainer: Gwenaëlle Lemoine <lemoine.gwenaelle at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GWENA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GWENA")

 

HTML	R Script	GWENA-vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, Sequencing, Software, Transcriptomics, Visualization, mRNAMicroarray
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment(>= 1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>= 4.0.4), methods, graphics, stats, utils
LinkingTo
Suggests	testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors(>= 0.22.1), BiocStyle(>= 2.15.8)
SystemRequirements
Enhances
URL
BugReports	https://github.com/Kumquatum/GWENA/issues
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GWENA_1.2.0.tar.gz
Windows Binary	GWENA_1.2.0.zip
macOS 10.13 (High Sierra)	GWENA_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GWENA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GWENA
Package Short Url	https://bioconductor.org/packages/GWENA/
Package Downloads Report	Download Stats