DESCRIPTION

Package: oncoEnrichR
Type: Package
Title: Cancer-dedicated gene set interpretation
Version: 1.5.2
Authors@R: person(given = "Sigve", family = "Nakken", role = c("aut", "cre"),
             email = "sigven@ifi.uio.no",
             comment = c(ORCID = "0000-0001-8468-2050"))
Maintainer: Sigve Nakken <sigven@ifi.uio.no>
URL: https://sigven.github.io/oncoEnrichR
BugReports: https://github.com/sigven/oncoEnrichR/issues
Description: oncoEnrichR performs annotation and prioritization of genesets 
    discovered from high-throughput experiments within cancer biology. The tool 
    queries a number of high-quality resources, including DepMap/Project Score 
    (cellular fitness in genome-scale drop-out screens), Open Targets Platform 
    (comprehensive target-drug associations, cancer hallmark evidence and 
    target-tumor type associations), TCGA (genetic aberrations and gene co-expression 
    patterns in human tumor samples), STRING/BioGRID (protein-protein interaction networks), 
    curated protein complexes (CORUM/Compleat/ComplexPortal/hu.MAP2), 
    COMPARTMENTS (subcellular compartments), 
    Human Protein Atlas (prognostic gene expression associations), CellChatDB (ligand-receptor interactions),
    DoRothEA (regulatory interactions), synthetic lethality predictions, 
    and Gene Ontology/MSigDB/REACTOME/KEGG/NetPath 
    (functional enrichment/over-representation analysis with respect to gene 
    function and cellular pathways). The package outputs both an interactive HTML 
    report and an Excel workbook in which the user can interrogate the various 
    types of annotations and analyses performed with the query geneset. 
Depends: 
    R (>= 4.1)
biocViews: 
Imports: dplyr,
         assertthat,
         assertable,
         clusterProfiler,
         DT, 
         gganatogram, 
         ggpubr,
         openxlsx,
         stringr,
         tidyr,
         readr,
         googledrive,
         visNetwork, 
         quarto,
         plotly, 
         jsonlite,
         forcats,
         org.Hs.eg.db, 
         igraph (>= 2.0), 
         lgr,
         maftools, 
         rlang,
         textclean (>= 0.9.3)
Suggests: 
    testthat (>= 3.1.0),
    knitr,
    rmarkdown
VignetteBuilder: knitr 
License: MIT + file LICENSE
Encoding: UTF-8
Remotes: jespermaag/gganatogram
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
LazyData: true
SystemRequirements: Quarto command line tool
    (<https://github.com/quarto-dev/quarto-cli>).