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 (>= 4.6.0)
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
git_url: https://git.bioconductor.org/packages/ctdR
git_branch: devel
git_last_commit: 57961d5
git_last_commit_date: 2026-10-04
Repository: Bioconductor 3.24
Date/Publication: 2026-10-05
NeedsCompilation: no
Packaged: 2026-10-05 21:08:46 UTC; biocbuild
Author: Luigi Corsaro [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1218-230X>)
Maintainer: Luigi Corsaro <lcorsaro69@gmail.com>
