Package: cosmosR
Type: Package
Title: COSMOS (Causal Oriented Search of Multi-Omic Space)
Version: 1.20.0
Description: COSMOS (Causal Oriented Search of Multi-Omic Space) is a
        method that integrates phosphoproteomics, transcriptomics, and
        metabolomics data sets based on prior knowledge of signaling,
        metabolic, and gene regulatory networks. It estimated the
        activities of transcrption factors and kinases and finds a
        network-level causal reasoning. Thereby, COSMOS provides
        mechanistic hypotheses for experimental observations across
        mulit-omics datasets.
Authors@R: c(
    person(given = "Aurélien",
           family = "Dugourd",
           role = c("aut", "cre"),
           email = "dugourd@ebi.ac.uk",
           comment = c(ORCID = "0000-0002-0714-028X")),
    person(given = "Attila",
           family = "Gabor",
           role = c("aut"),
           email = "attila.gabor@uni-heidelberg.de",
           comment = c(ORCID = "0000-0002-0776-1182")),
    person(given = "Katharina",
           family = "Zirngibl",
           role = c("aut"),
           email = "katharina.zirngibl@uni-heidelberg.de",
           comment = c(ORCID = "0000-0002-7518-0339")))
URL: https://github.com/saezlab/COSMOSR
BugReports: https://github.com/saezlab/COSMOSR/issues
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr,
        rlang, stringr, utils, visNetwork, decoupleR
Suggests: testthat, knitr, rmarkdown, htmltools, markdown, ggplot2,
        stringi, reshape2
biocViews: CellBiology, Pathways, Network, Proteomics, Metabolomics,
        Transcriptomics, GeneSignaling
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:56:03 UTC
RemoteUrl: https://github.com/bioc/cosmosR
RemoteRef: RELEASE_3_23
RemoteSha: 3fdc39f5a32d0187d8e3081be4cf8063d9e8ad92
NeedsCompilation: no
Packaged: 2026-10-10 16:06:28 UTC; root
Author: Aurélien Dugourd [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0714-028X>),
  Attila Gabor [aut] (ORCID: <https://orcid.org/0000-0002-0776-1182>),
  Katharina Zirngibl [aut] (ORCID:
    <https://orcid.org/0000-0002-7518-0339>)
Maintainer: Aurélien Dugourd <dugourd@ebi.ac.uk>