Package: SPONGE
Type: Package
Title: Sparse Partial Correlations On Gene Expression
Version: 1.34.0
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"),
           person(given = "Azim Dehghani",
           family = "Amirabad"),
           person(given = "Dennis",
           family = "Kostka"),
           person(given = "Marcel H.",
           family = "Schulz"))
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
RoxygenNote: 7.1.2
Depends: R (>= 3.6)
Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra,
        digest, doParallel, bigmemory, GSVA
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
VignetteBuilder: knitr
biocViews: GeneExpression, Transcription, GeneRegulation,
        NetworkInference, Transcriptomics, SystemsBiology, Regression,
        RandomForest, MachineLearning
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev
        libxml2-dev libssl-dev perl libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:46:16 UTC
RemoteUrl: https://github.com/bioc/SPONGE
RemoteRef: RELEASE_3_23
RemoteSha: 969b6aad8d3eca08141b8b023a3b692f15a10b32
NeedsCompilation: no
Packaged: 2026-05-30 09:11:04 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>)
Maintainer: Markus List <markus.list@tum.de>
Built: R 4.6.0; ; 2026-05-30 12:46:25 UTC; unix
