Package: progeny
Title: Pathway RespOnsive GENes for activity inference from gene expression
Version: 1.33.0
Authors@R: c(
    person(given = "Michael",
           family = "Schubert",
           role = "aut"),
    person(given = "Alberto",
           family = "Valdeolivas",
           role = "ctb",
           email = "alvaldeolivas@gmail.com",
           comment = c(ORCID = "0000-0001-5482-9023")),
    person(given = "Christian H.",
           family = "Holland",
           role = "ctb",
           email = "cholland2408@gmail.com",
           comment = c(ORCID = "0000-0002-3060-5786")),
    person(given = "Igor",
           family = "Bulanov",
           role = "ctb"),
    person(given = "Aurélien",
           family = "Dugourd",
           role = c("cre","ctb"), 
           email = "aurelien.dugourd@bioquant.uni-heidelberg.de")
           )
Description: PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics. 
URL: https://github.com/saezlab/progeny
BugReports: https://github.com/saezlab/progeny/issues
Depends:
    R (>= 3.6.0)
Imports:
    Biobase,
    stats, 
    dplyr,
    tidyr,
    ggplot2,
    ggrepel,
    gridExtra,
    decoupleR,
    reshape2
biocViews: SystemsBiology, GeneExpression, FunctionalPrediction, GeneRegulation
License: Apache License (== 2.0) | file LICENSE
LazyData: true
LazyDataCompression: bzip2
Encoding: UTF-8
Suggests:
    airway,
    biomaRt,
    BiocFileCache,
    broom,
    Seurat,
    SingleCellExperiment,
    DESeq2,
    BiocStyle,
    knitr,
    readr,
    readxl,
    pheatmap,
    tibble,
    rmarkdown,
    testthat (>= 2.1.0)
VignetteBuilder: knitr
RoxygenNote: 7.1.2
git_url: https://git.bioconductor.org/packages/progeny
git_branch: devel
git_last_commit: 397f983
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
