GWENA

DOI: 10.18129/B9.bioc.GWENA    

This is the development version of GWENA; for the stable release version, see GWENA.

Pipeline for augmented co-expression analysis

Bioconductor version: Development (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: 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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews	Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, Sequencing, Software, Transcriptomics, Visualization, mRNAMicroarray
Version	1.9.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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