Bioconductor release scheduled for October 29

GWENA

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

Pipeline for augmented co-expression analysis


Bioconductor version: Development (3.22)

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] ORCID iD ORCID: 0000-0003-4747-1937 , 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 "4.5") 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

Details

biocViews Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, Sequencing, Software, Transcriptomics, Visualization, mRNAMicroarray
Version 1.19.0
In Bioconductor since BioC 3.12 (R-4.0) (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)
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Package Archives

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

Source Package GWENA_1.19.0.tar.gz
Windows Binary (x86_64) GWENA_1.19.0.zip
macOS Binary (x86_64) GWENA_1.19.0.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/GWENA/
Package Short Url https://bioconductor.org/packages/GWENA/
Package Downloads Report Download Stats