GmicR

DOI: 10.18129/B9.bioc.GmicR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GmicR.

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

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	GmicR_vignette
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Bayesian, Clustering, GUI, GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, QualityControl, Software, SystemsBiology
Version	1.6.0
In Bioconductor since	BioC 3.10 (R-3.6) (2 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
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GmicR_1.6.0.tar.gz
Windows Binary	GmicR_1.6.0.zip
macOS 10.13 (High Sierra)	GmicR_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GmicR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GmicR
Package Short Url	https://bioconductor.org/packages/GmicR/
Package Downloads Report	Download Stats