Type: Package
Package: decoupleR
Title: decoupleR: Ensemble of computational methods to infer biological
        activities from omics data
Version: 2.16.0
Authors@R: 
    c(person(given = "Pau",
             family = "Badia-i-Mompel",
             role = c("aut","cre"),
             email = "pau.badia@uni-heidelberg.de",
             comment = c(ORCID = "0000-0002-1004-3923")),
      person(given = "Jesús",
             family = "Vélez-Santiago",
             role = c("aut"),
             email = "jvelezmagic@gmail.com",
             comment = c(ORCID = "0000-0001-5128-3838")),
      person(given = "Jana",
             family = "Braunger",
             role = c("aut"),
             email = "jana.bc@gmx.de",
             comment = c(ORCID = "0000-0003-0820-9987")),
      person(given = "Celina",
             family = "Geiss",
             role = c("aut"),
             email = "celina.geiss@stud.uni-heidelberg.de",
             comment = c(ORCID = "0000-0002-8740-706X")),
      person(given = "Daniel",
             family = "Dimitrov",
             role = c("aut"),
             email = "daniel.dimitrov@uni-heidelberg.de",
             comment = c(ORCID = "0000-0002-5197-2112")),
      person(given = "Sophia",
             family = "Müller-Dott",
             role = c("aut"),
             email = "sophia.mueller-dott@uni-heidelberg.de",
             comment = c(ORCID = "0000-0002-9710-1865")),
      person(given = "Petr",
             family = "Taus",
             role = c("aut"),
             email = "petr.taus@ceitec.muni.cz",
             comment = c(ORCID = "0000-0003-3764-9033")),
      person(given = "Aurélien",
             family = "Dugourd",
             role = c("aut"),
             email = "aurelien.dugourd@bioquant.uni-heidelberg.de",
             comment = c(ORCID = "0000-0002-0714-028X")),
      person(given = "Christian H.",
             family = "Holland",
             role = "aut",
             email = "cholland2408@gmail.com",
             comment = c(ORCID = "0000-0002-3060-5786")),
      person(given = "Ricardo O.",
             family = "Ramirez Flores",
             role = c("aut"),
             email = "roramirezf@uni-heidelberg.de ",
             comment = c(ORCID = "0000-0003-0087-371X")),
      person(given = "Julio",
             family = "Saez-Rodriguez",
             role = c("aut"),
             email = "pub.saez@uni-heidelberg.de",
             comment = c(ORCID = "0000-0002-8552-8976"))
             )
Description: Many methods allow us to extract biological activities
        from omics data using information from prior knowledge
        resources, reducing the dimensionality for increased
        statistical power and better interpretability. Here, we present
        decoupleR, a Bioconductor package containing different
        statistical methods to extract these signatures within a
        unified framework. decoupleR allows the user to flexibly test
        any method with any resource. It incorporates methods that take
        into account the sign and weight of network interactions.
        decoupleR can be used with any omic, as long as its features
        can be linked to a biological process based on prior knowledge.
        For example, in transcriptomics gene sets regulated by a
        transcription factor, or in phospho-proteomics phosphosites
        that are targeted by a kinase.
License: GPL-3 + file LICENSE
URL: https://saezlab.github.io/decoupleR/
BugReports: https://github.com/saezlab/decoupleR/issues
Depends: R (>= 4.0)
Imports: BiocParallel, broom, dplyr, magrittr, Matrix, parallelly,
        purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr
Suggests: glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell,
        SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr,
        pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo,
        pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel,
        patchwork, magick
VignetteBuilder: knitr
biocViews: DifferentialExpression, FunctionalGenomics, GeneExpression,
        GeneRegulation, Network, Software, StatisticalMethod,
        Transcription,
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0
Config/pak/sysreqs: libicu-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:09:41 UTC
RemoteUrl: https://github.com/bioc/decoupleR
RemoteRef: RELEASE_3_22
RemoteSha: ff3aa1d8dac686c11b8611a840a2b5cf30df6902
NeedsCompilation: no
Packaged: 2025-11-11 13:58:34 UTC; root
Author: Pau Badia-i-Mompel [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1004-3923>),
  Jesús Vélez-Santiago [aut] (ORCID:
    <https://orcid.org/0000-0001-5128-3838>),
  Jana Braunger [aut] (ORCID: <https://orcid.org/0000-0003-0820-9987>),
  Celina Geiss [aut] (ORCID: <https://orcid.org/0000-0002-8740-706X>),
  Daniel Dimitrov [aut] (ORCID: <https://orcid.org/0000-0002-5197-2112>),
  Sophia Müller-Dott [aut] (ORCID:
    <https://orcid.org/0000-0002-9710-1865>),
  Petr Taus [aut] (ORCID: <https://orcid.org/0000-0003-3764-9033>),
  Aurélien Dugourd [aut] (ORCID: <https://orcid.org/0000-0002-0714-028X>),
  Christian H. Holland [aut] (ORCID:
    <https://orcid.org/0000-0002-3060-5786>),
  Ricardo O. Ramirez Flores [aut] (ORCID:
    <https://orcid.org/0000-0003-0087-371X>),
  Julio Saez-Rodriguez [aut] (ORCID:
    <https://orcid.org/0000-0002-8552-8976>)
Maintainer: Pau Badia-i-Mompel <pau.badia@uni-heidelberg.de>
Built: R 4.5.2; ; 2025-11-11 14:08:30 UTC; windows
