SRGnet
This package is for version 3.9 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 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>
citation("SRGnet")):
Installation
To install this package, start R (version "3.6") 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 |
Details
| biocViews | Regression, Software, StatisticalMethod |
| Version | 1.10.0 |
| 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 | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.9 | Source Archive |