Welcome to the new bioconductor.org!

GWENA

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

Pipeline for augmented co-expression analysis


Bioconductor version: Development (3.19)

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 "4.4") 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")
GWENA-vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, Sequencing, Software, Transcriptomics, Visualization, mRNAMicroarray
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
System Requirements
URL
Bug Reports https://github.com/Kumquatum/GWENA/issues
See More
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)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GWENA_1.13.0.tar.gz
Windows Binary GWENA_1.13.0.zip
macOS Binary (x86_64) GWENA_1.13.0.tgz
macOS Binary (arm64) GWENA_1.13.0.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/
Package Downloads Report Download Stats