GmicR

This is the released version of GmicR; for the devel version, see GmicR.

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

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DOI: 10.18129/B9.bioc.GmicR

Bioconductor version: Release (3.22)

This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool.

Author: Richard Virgen-Slane

Maintainer: Richard Virgen-Slane <RVS.BioTools at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("GmicR")

GmicR_vignette HTML R Script

Reference Manual PDF

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, Clustering, GUI, GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, QualityControl, Software, SystemsBiology

Version 1.24.0

In Bioconductor since BioC 3.10 (R-3.6) (6 years)

License GPL-2 + file LICENSE

Depends

Imports AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils

System Requirements

URL

Suggests knitr, rmarkdown, testthat

Linking To

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Package Archives

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

Source Package GmicR_1.24.0.tar.gz

Windows Binary (x86_64) GmicR_1.24.0.zip

macOS Binary (x86_64) GmicR_1.24.0.tgz

macOS Binary (arm64) GmicR_1.24.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/GmicR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GmicR

Bioc Package Browser https://code.bioconductor.org/browse/GmicR/

Package Short Url https://bioconductor.org/packages/GmicR/

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