SPONGE

This is the development version of SPONGE; for the stable release version, see SPONGE.

Sparse Partial Correlations On Gene Expression

Bioconductor version: Development (3.21)

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] (ORCID: ), Markus Hoffmann [aut] (ORCID: ), Lena Strasser [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneRegulation, MachineLearning, NetworkInference, RandomForest, Regression, Software, SystemsBiology, Transcription, Transcriptomics
Version	1.29.0
In Bioconductor since	BioC 3.6 (R-3.4) (7 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, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr
System Requirements
URL

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	SPONGE_1.29.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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