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GmicR

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

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Bayesian, Clustering, GUI, GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, QualityControl, Software, SystemsBiology
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 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
Linking To
Suggests knitr, rmarkdown, testthat
System Requirements
Enhances
URL
See More
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_1.14.0.tar.gz
Windows Binary GmicR_1.14.0.zip
macOS Binary (x86_64)
macOS Binary (arm64) GmicR_1.14.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive