SPONGE

DOI: 10.18129/B9.bioc.SPONGE    

Sparse Partial Correlations On Gene Expression

Bioconductor version: Release (3.6)

This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input.

Author: Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz

Maintainer: Markus List <markus.list at mpi-inf.mpg.de>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SPONGE")

Documentation

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription, Transcriptomics
Version	1.0.3
License	GPL (>=3)
Depends	R (>= 3.4)
Imports	Biobase, stats, ppcor, logging, foreach, doRNG, data.table, bigmemory, MASS, expm, gRbase, glmnet, igraph, iterators
LinkingTo
Suggests	testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel, gridExtra, digest, doParallel
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	SPONGE_1.0.3.tar.gz
Windows Binary	SPONGE_1.0.3.zip
Mac OS X 10.11 (El Capitan)	SPONGE_1.0.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SPONGE
Package Short Url	http://bioconductor.org/packages/SPONGE/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive