rTRM

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

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, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks

Bioconductor version: Release (3.23)

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

Author: Diego Diez

Maintainer: Diego Diez <diego10ruiz at gmail.com>

Citation (from within R, enter citation("rTRM")):

Diego Diez. rTRM: Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks. doi:10.18129/B9.bioc.rTRM, R package version 1.50.0, https://bioconductor.org/packages/rTRM.

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("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")

Introduction to rTRM	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneRegulation, GraphAndNetwork, Network, Software, Transcription
Version	1.50.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 years)
License	GPL-3
Depends	R (>= 2.10), igraph (>= 1.0)
Imports	methods, AnnotationDbi, DBI, RSQLite
System Requirements
URL	https://github.com/ddiez/rTRM
Bug Reports	https://github.com/ddiez/rTRM/issues

Suggests	RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me	rTRMui
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	rTRM_1.50.0.tar.gz
Windows Binary (x86_64)	rTRM_1.49.0.zip
macOS Binary (big-sur-x86_64)	rTRM_1.50.0.tgz
macOS Binary (sonoma-arm64)	rTRM_1.50.0.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