rTRM

DOI: 10.18129/B9.bioc.rTRM    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see rTRM.

Identification of transcriptional regulatory modules from PPI networks

Bioconductor version: 3.9

rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

Author: Diego Diez

Maintainer: Diego Diez <diego10ruiz at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rTRM")

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("rTRM")

 

PDF	R Script	Introduction to rTRM
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneRegulation, GraphAndNetwork, Network, Software, Transcription
Version	1.22.0
In Bioconductor since	BioC 2.13 (R-3.0) (6 years)
License	GPL-3
Depends	R (>= 2.10), igraph (>= 1.0)
Imports	AnnotationDbi, DBI, RSQLite
LinkingTo
Suggests	RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2
SystemRequirements
Enhances
URL	https://github.com/ddiez/rTRM
BugReports	https://github.com/ddiez/rTRM/issues
Depends On Me
Imports Me	rTRMui
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	rTRM_1.22.0.tar.gz
Windows Binary	rTRM_1.22.0.zip
Mac OS X 10.11 (El Capitan)	rTRM_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rTRM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rTRM
Package Short Url	https://bioconductor.org/packages/rTRM/
Package Downloads Report	Download Stats