GmicR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10

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

Bioconductor version: Release (3.23)

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")):

Richard Virgen-Slane. GmicR: Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC). doi:10.18129/B9.bioc.GmicR, R package version 1.26.0, https://bioconductor.org/packages/GmicR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.26.0
In Bioconductor since	BioC 3.10 (R-3.6) (7 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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	GmicR_1.26.0.tar.gz
Windows Binary (x86_64)	GmicR_1.26.0.zip
macOS Binary (big-sur-x86_64)	GmicR_1.26.0.tgz
macOS Binary (sonoma-arm64)	GmicR_1.26.0.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