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An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.

Author: Dario Tommasini [aut, cre] , Brent Fogel [aut, ctb]

Maintainer: Dario Tommasini <dtommasini0 at gmail.com>

Citation (from within R, enter citation("multiWGCNA")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Astrocyte multiWGCNA network HTML R Script
General Workflow HTML R Script
Reference Manual PDF


biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Regression, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3
Depends R (>= 4.3.0), ggalluvial
Imports stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment
System Requirements
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Suggests BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan
Linking To
Depends On Me
Imports Me
Suggests Me multiWGCNAdata
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Package Archives

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

Source Package multiWGCNA_1.0.0.tar.gz
Windows Binary multiWGCNA_1.0.0.zip
macOS Binary (x86_64) multiWGCNA_1.0.0.tgz
macOS Binary (arm64) multiWGCNA_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/multiWGCNA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/multiWGCNA
Bioc Package Browser https://code.bioconductor.org/browse/multiWGCNA/
Package Short Url https://bioconductor.org/packages/multiWGCNA/
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