SPONGE

DOI: 10.18129/B9.bioc.SPONGE    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see SPONGE.

Sparse Partial Correlations On Gene Expression

Bioconductor version: 3.11

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>

Installation

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

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

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	1.10.0
In Bioconductor since	BioC 3.6 (R-3.4) (3 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_1.10.0.tar.gz
Windows Binary	SPONGE_1.10.0.zip
macOS 10.13 (High Sierra)	SPONGE_1.10.0.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