Package: cosmosR
Type: Package
Title: COSMOS (Causal Oriented Search of Multi-Omic Space)
Version: 1.21.2
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,
        https://saezlab.github.io/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
SystemRequirements: pandoc (>= 2.8) - https://pandoc.org
Imports: CARNIVAL, 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: https://bioc.r-universe.dev
Date/Publication: 2026-09-03 09:31:50 UTC
RemoteUrl: https://github.com/bioc/cosmosR
RemoteRef: HEAD
RemoteSha: b2ed195738479c4ad204cace37fd11ae2fd02bb8
NeedsCompilation: no
Packaged: 2026-09-14 11:39:31 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>