DESCRIPTION

Package: cosmosR
Type: Package
Title: COSMOS (Causal Oriented Search of Multi-Omic Space)
Version: 1.9.1
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,
    htmltools,
    markdown,
    piano,
    ggplot2,
    stringi,
    reshape2
biocViews: CellBiology, Pathways, Network, Proteomics, Metabolomics, Transcriptomics,
    GeneSignaling