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

Sparse Partial Correlations On Gene Expression

Bioconductor version: Development (3.19)

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>

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


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biocViews GeneExpression, GeneRegulation, MachineLearning, NetworkInference, RandomForest, Regression, Software, SystemsBiology, Transcription, Transcriptomics
Version 1.25.0
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
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Suggests testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA
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Imports Me miRspongeR
Suggests Me mirTarRnaSeq
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