GWENA
This is thereleased version of GWENA; for the devel version, seeGWENA.
Pipeline for augmented co-expression analysis
Bioconductor version: Release (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: Gwenaëlle Lemoine [aut, cre]
ORCID: 0000-0003-4747-1937, 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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("GWENA")For older versions of R, please refer to the appropriateBioconductor 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 | 1.20.0 |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | GWENA_1.20.0.tar.gz |
| Windows Binary (x86_64) | GWENA_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | GWENA_1.20.0.tgz |
| macOS Binary (arm64) | GWENA_1.20.0.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 |