GWENA

DOI: 10.18129/B9.bioc.GWENA  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GWENA.

Pipeline for augmented co-expression analysis

Bioconductor version: 3.17

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

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

Citation (from within R, enter citation("GWENA")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.1)
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
Depends On Me
Imports Me
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Build Report  

Package Archives

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

Source Package GWENA_1.10.0.tar.gz
Windows Binary GWENA_1.10.0.zip
macOS Binary (x86_64) GWENA_1.10.0.tgz
macOS Binary (arm64) GWENA_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GWENA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GWENA
Bioc Package Browser https://code.bioconductor.org/browse/GWENA/
Package Short Url https://bioconductor.org/packages/GWENA/
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