Package: ctdR
Type: Package
Title: Enrichment Analysis of Chemical-Gene Interactions from the
        Comparative Toxicogenomics Database
Version: 0.99.11
Authors@R: person(
    given = "Luigi",
    family = "Corsaro",
    role = c("aut", "cre"),
    email = "lcorsaro69@gmail.com",
    comment = c(ORCID = "0000-0003-1218-230X"))
Description: Identifies chemicals significantly associated with a set
        of genes using data from the Comparative Toxicogenomics
        Database (CTD, <https://ctdbase.org>). Supports four enrichment
        methods through a unified interface: Over-Representation
        Analysis (ORA) via a hypergeometric test on stats::phyper(),
        Gene Set Enrichment Analysis (GSEA) via 'fgsea', the
        competitive gene-set test CAMERA via 'limma', and per-sample
        Gene Set Variation Analysis (GSVA) via 'GSVA'. Users download
        the CTD chemical-gene interactions file once, import it with
        import_CTD(), and then run enrichment_CTD() on either a gene
        list (ORA, GSEA) or an expression matrix (CAMERA, GSVA). This
        package does not bundle or redistribute CTD data. Users must
        download the required data files directly from
        <https://ctdbase.org> and comply with the CTD data licensing
        terms (see <https://ctdbase.org/about/legal.jsp>).
License: Apache License 2.0 | file LICENSE
URL: https://luigicorsaro.com/ctdR/, https://github.com/drake69/ctdR
BugReports: https://github.com/drake69/ctdR/issues
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: fgsea, ggplot2, readr, org.Hs.eg.db, AnnotationDbi, limma,
        GSVA, stats, BiocIO, BiocFileCache, S4Vectors,
        SummarizedExperiment, methods
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
biocViews: GeneSetEnrichment, Pathways, Annotation, GeneExpression,
        DataImport
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-04 05:32:40 UTC
RemoteUrl: https://github.com/bioc/ctdR
RemoteRef: HEAD
RemoteSha: 57961d56c89dda51cec7c8dcc4c91ed89f454aa2
NeedsCompilation: no
Packaged: 2026-10-30 21:23:44 UTC; root
Author: Luigi Corsaro [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1218-230X>)
Maintainer: Luigi Corsaro <lcorsaro69@gmail.com>