GmicR
This package is for version 3.12 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: 3.12
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("GmicR")):
Installation
To install this package, start R (version "4.0") 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 | ||
| LICENSE | Text |
Details
| biocViews | Bayesian, Clustering, GUI, GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, QualityControl, Software, SystemsBiology |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 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 |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GmicR_1.4.0.tar.gz |
| Windows Binary | GmicR_1.4.0.zip |
| macOS 10.13 (High Sierra) | GmicR_1.4.0.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 3.12 | Source Archive |