multiWGCNA

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see multiWGCNA.

multiWGCNA

Bioconductor version: 3.20

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] ORCID iD ORCID: 0000-0002-1214-6547 , Brent Fogel [aut, ctb]

Maintainer: Dario Tommasini <dtommasini0 at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("multiWGCNA")

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("multiWGCNA")

Astrocyte multiWGCNA network HTML R Script

General Workflow HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, DifferentialExpression, GeneExpression, RNASeq, Regression, Sequencing, Software

Version 1.4.0

In Bioconductor since BioC 3.18 (R-4.3) (1.5 years)

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

URL

Suggests BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me multiWGCNAdata

Links To Me

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Package Archives

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

Source Package multiWGCNA_1.4.0.tar.gz

Windows Binary (x86_64) multiWGCNA_1.4.0.zip

macOS Binary (x86_64) multiWGCNA_1.4.0.tgz

macOS Binary (arm64) multiWGCNA_1.4.0.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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