SPONGE

DOI: 10.18129/B9.bioc.SPONGE    

This is the development version of SPONGE; to use it, please install the devel version of Bioconductor.

Sparse Partial Correlations On Gene Expression

Bioconductor version: Development (3.10)

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 wzw.tum.de>

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SPONGE")

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("SPONGE")

 

HTML R Script Vignette Title
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, GeneRegulation, NetworkInference, Regression, Software, SystemsBiology, Transcription, Transcriptomics
Version 1.7.1
In Bioconductor since BioC 3.6 (R-3.4) (2 years)
License GPL (>=3)
Depends R (>= 3.4)
Imports Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators
LinkingTo
Suggests testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel, gridExtra, digest, doParallel, bigmemory
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 SPONGE_1.7.1.tar.gz
Windows Binary SPONGE_1.7.1.zip
Mac OS X 10.11 (El Capitan) SPONGE_1.7.1.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

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