SRGnet

DOI: 10.18129/B9.bioc.SRGnet    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SRGnet.

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

Bioconductor version: 3.14

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 "4.1") and enter:

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

BiocManager::install("SRGnet")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Regression, Software, StatisticalMethod
Version	1.20.0
In Bioconductor since	BioC 3.4 (R-3.3) (5.5 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
Windows Binary
macOS 10.13 (High Sierra)
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