SRGnet

This package is for version 3.11 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: 3.11

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>

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

Installation

To install this package, start R (version "4.0") 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

To view documentation for the version of this package installed in your system, start R and enter:

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

Details

biocViews Regression, Software, StatisticalMethod
Version 1.14.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package SRGnet_1.14.0.tar.gz
Windows Binary SRGnet_1.14.0.zip
macOS 10.13 (High Sierra) SRGnet_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SRGnet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SRGnet
Bioc Package Browser https://code.bioconductor.org/browse/SRGnet/
Package Short Url https://bioconductor.org/packages/SRGnet/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive