Package: SPONGE
Type: Package
Title: Sparse Partial Correlations On Gene Expression
Version: 1.33.0
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 libwebp-dev libxml2-dev
        libssl-dev perl libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:40:24 UTC
RemoteUrl: https://github.com/bioc/SPONGE
RemoteRef: HEAD
RemoteSha: 6ba4e2dfdef62fe1d9a24a7c7996d2ac3b8c5cba
NeedsCompilation: no
Packaged: 2026-02-21 07:46:53 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; ; 2026-02-21 07:50:04 UTC; unix
