SPONGE

DOI: 10.18129/B9.bioc.SPONGE  

Sparse Partial Correlations On Gene Expression

Bioconductor version: Release (3.17)

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. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Author: Markus List [aut, cre] , Markus Hoffmann [aut]

Maintainer: Markus List <markus.list at tum.de>

Installation

To install this package, start R (version "4.3") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SPONGE")

 

HTML	R Script	SPONGE vignette
HTML	R Script	spongEffects vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneRegulation, MachineLearning, NetworkInference, RandomForest, Regression, Software, SystemsBiology, Transcription, Transcriptomics
Version	1.22.0
In Bioconductor since	BioC 3.6 (R-3.4) (6 years)
License	GPL (>=3)
Depends	R (>= 3.6)
Imports	Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, miRBaseConverter, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr
LinkingTo
Suggests	testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	miRspongeR
Suggests Me	mirTarRnaSeq
Links To Me
Build Report

Package Archives

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

Source Package	SPONGE_1.22.0.tar.gz
Windows Binary	SPONGE_1.22.0.zip
macOS Binary (x86_64)	SPONGE_1.22.0.tgz
macOS Binary (arm64)	SPONGE_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SPONGE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SPONGE
Bioc Package Browser	https://code.bioconductor.org/browse/SPONGE/
Package Short Url	https://bioconductor.org/packages/SPONGE/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive