SPONGE

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see SPONGE.

Sparse Partial Correlations On Gene Expression


Bioconductor version: 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>

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

Installation

To install this package, start R (version "3.4") and enter:


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

BiocManager::install("SPONGE")

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

Documentation

Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription, Transcriptomics
Version 1.0.3
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>=3)
Depends R (>= 3.4)
Imports Biobase, stats, ppcor, logging, foreach, doRNG, data.table, bigmemory, MASS, expm, gRbase, glmnet, igraph, iterators
System Requirements
URL
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Suggests testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel, gridExtra, digest, doParallel
Linking To
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Depends On Me
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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
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SPONGE
Package Short Url https://bioconductor.org/packages/SPONGE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive