SRGnet

DOI: 10.18129/B9.bioc.SRGnet    

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

SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data from transcriptomics data

Bioconductor version: 3.9

We developed SRGnet to analyze synergistic regulatory mechanisms in transcriptome profiles that act to enhance the overall cell response to combination of mutations, drugs or environmental exposure. This package can be used to identify regulatory modules downstream of synergistic response genes, prioritize synergistic regulatory genes that may be potential intervention targets, and contextualize gene perturbation experiments.

Author: Isar Nassiri [aut, cre], Matthew McCall [aut, cre]

Maintainer: Isar Nassiri <isar_nassiri at urmc.rochester.edu>

Installation

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

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

BiocManager::install("SRGnet")

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("SRGnet")

 

HTML		SRGnet An R package for studying synergistic response to gene mutations from transcriptomics data \
PDF		Reference Manual

Details

biocViews	Regression, Software, StatisticalMethod
Version	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	GPL-2
Depends	R (>= 3.3.1), EBcoexpress, MASS, igraph, pvclust (>= 2.0-0), gbm (>= 2.1.1), limma, DMwR (>= 0.4.1), matrixStats, Hmisc
Imports
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
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	SRGnet_1.10.0.tar.gz
Windows Binary	SRGnet_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	SRGnet_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SRGnet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SRGnet
Package Short Url	https://bioconductor.org/packages/SRGnet/
Package Downloads Report	Download Stats