GWENA
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GWENA.
Pipeline for augmented co-expression analysis
Bioconductor version: 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>
citation("GWENA")):
Installation
To install this package, start R (version "4.1") 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")| GWENA-vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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) (3.5 years) |
| 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 |
| 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_1.2.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/GWENA/ |
| Package Short Url | https://bioconductor.org/packages/GWENA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |