SPONGE

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see SPONGE.

Sparse Partial Correlations On Gene Expression

Bioconductor version: 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 iD ORCID: 0000-0002-0941-4168 , Markus Hoffmann [aut] ORCID iD ORCID: 0000-0002-1920-288X , Lena Strasser [aut] ORCID iD ORCID: 0009-0007-7881-6818

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")
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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, GeneRegulation, MachineLearning, NetworkInference, RandomForest, Regression, Software, SystemsBiology, Transcription, Transcriptomics

Version 1.30.0

In Bioconductor since BioC 3.6 (R-3.4) (8 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_1.30.0.tar.gz

Windows Binary (x86_64) SPONGE_1.30.0.zip

macOS Binary (x86_64) SPONGE_1.30.0.tgz

macOS Binary (arm64) SPONGE_1.30.0.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/

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