Package: SPONGE
Type: Package
Title: Sparse Partial Correlations On Gene Expression
Version: 1.30.0
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
git_url: https://git.bioconductor.org/packages/SPONGE
git_branch: RELEASE_3_21
git_last_commit: 2b36767
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-15 23:52:10 UTC; biocbuild
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 4.5.0; ; 2025-04-16 06:30:40 UTC; unix
