Package: SPONGE
Type: Package
Title: Sparse Partial Correlations On Gene Expression
Version: 1.35.3
Encoding: UTF-8
Authors@R: c(person(given = "Markus",
           family = "List",
           role = c("aut", "cre"),
           email = "markus.list@tum.de",
           comment = c(ORCID = "0000-0002-0941-4168")),
           person(given = "Markus",
           family = "Hoffmann",
           role = c("aut"),
           email = "markus.hoffmann@nih.gov",
           comment = c(ORCID = "0000-0002-1920-288X")),
           person(given = "Lena",
           family = "Strasser",
           role = c("aut"),
           email = "lena.j.strasser@tum.de",
           comment = c(ORCID = "0009-0007-7881-6818")),
           person(given = "Fabio",
           family = "Boniolo",
           role = c("aut")),
           person(given = "Azim Dehghani",
           family = "Amirabad",
           role = c("aut")),
           person(given = "Dennis",
           family = "Kostka",
           role = c("aut")),
           person(given = "Marcel H.",
           family = "Schulz",
           role = c("aut")))
Description: 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.
License: GPL (>=3)
LazyData: TRUE
LazyDataCompression: xz
Depends: R (>= 3.6)
Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra,
        digest, doParallel, bigmemory, GSVA
Imports: methods, Biobase, stats, ppcor, logger, foreach, doRNG,
        data.table, MASS, expm, gRbase, glmnet, igraph, iterators,
        caret, dplyr, biomaRt, randomForest, ggridges, cvms,
        ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr,
        stringr, tidyr, tibble
VignetteBuilder: knitr
biocViews: GeneExpression, Transcription, GeneRegulation,
        NetworkInference, Transcriptomics, SystemsBiology, Regression,
        RandomForest, MachineLearning
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libxml2-dev libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-01 13:44:15 UTC
RemoteUrl: https://github.com/bioc/SPONGE
RemoteRef: HEAD
RemoteSha: 48ad8f6a345400acedfab41bdf0bc4b33f4fc2ee
NeedsCompilation: no
Packaged: 2026-06-01 21:07:27 UTC; root
Author: Markus List [aut, cre] (ORCID: <https://orcid.org/0000-0002-0941-4168>),
  Markus Hoffmann [aut] (ORCID: <https://orcid.org/0000-0002-1920-288X>),
  Lena Strasser [aut] (ORCID: <https://orcid.org/0009-0007-7881-6818>),
  Fabio Boniolo [aut],
  Azim Dehghani Amirabad [aut],
  Dennis Kostka [aut],
  Marcel H. Schulz [aut]
Maintainer: Markus List <markus.list@tum.de>