GWENA
This is the development version of GWENA; for the stable release version, see GWENA.
Pipeline for augmented co-expression analysis
Bioconductor version: Development (3.24)
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")):Gwenaëlle Lemoine. GWENA: Pipeline for augmented co-expression analysis. doi:10.18129/B9.bioc.GWENA, R package version 1.23.0, https://bioconductor.org/packages/GWENA.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, Sequencing, Software, Transcriptomics, Visualization, mRNAMicroarray |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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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| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GWENA_1.23.0.tar.gz |
| Windows Binary (x86_64) | GWENA_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | GWENA_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | GWENA_1.23.0.tgz |
| 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 |