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SPONGE

Sparse Partial Correlations On Gene Expression


Bioconductor version: Release (3.18)

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>

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

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

Reference Manual PDF

Details

biocViews GeneExpression, GeneRegulation, MachineLearning, NetworkInference, RandomForest, Regression, Software, SystemsBiology, Transcription, Transcriptomics
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
System Requirements
URL
See More
Suggests testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA
Linking To
Enhances
Depends On Me
Imports Me miRspongeR
Suggests Me mirTarRnaSeq
Links To Me
Build Report Build Report

Package Archives

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

Source Package
Windows Binary SPONGE_1.24.0.zip
macOS Binary (x86_64) SPONGE_1.24.0.tgz
macOS Binary (arm64) SPONGE_1.24.0.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