Package: cosmosR
Type: Package
Title: COSMOS (Causal Oriented Search of Multi-Omic Space)
Version: 1.18.1
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"),
           email = "dugourdaurelien@gmail.com",
           comment = c(ORCID = "0000-0002-0714-028X")),
    person(given = "Attila",
           family = "Gabor",
           role = c("cre"),
           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: 7.2.3
VignetteBuilder: knitr
Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr,
        rlang, stringr, utils, visNetwork, decoupleR
Suggests: testthat, knitr, rmarkdown, piano, ggplot2
biocViews: CellBiology, Pathways, Network, Proteomics, Metabolomics,
        Transcriptomics, GeneSignaling
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-02-10 12:59:12 UTC
RemoteUrl: https://github.com/bioc/cosmosR
RemoteRef: RELEASE_3_22
RemoteSha: 80dd9b7e0e0467405a9f0ee88654676468dcf108
NeedsCompilation: no
Packaged: 2026-02-14 07:42:06 UTC; root
Author: Aurélien Dugourd [aut] (ORCID: <https://orcid.org/0000-0002-0714-028X>),
  Attila Gabor [cre] (ORCID: <https://orcid.org/0000-0002-0776-1182>),
  Katharina Zirngibl [aut] (ORCID:
    <https://orcid.org/0000-0002-7518-0339>)
Maintainer: Attila Gabor <attila.gabor@uni-heidelberg.de>
Built: R 4.5.2; ; 2026-02-14 07:44:15 UTC; windows
