# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# ------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "ctdR" in publications use:'
type: software
license: Apache-2.0
title: 'ctdR: Enrichment Analysis of Chemical-Gene Interactions from the Comparative
  Toxicogenomics Database'
version: 0.99.11
doi: 10.5281/zenodo.19344200
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ctdR
abstract: '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>).'
authors:
- family-names: Corsaro
  given-names: Luigi
  email: lcorsaro69@gmail.com
  orcid: https://orcid.org/0000-0003-1218-230X
preferred-citation:
  type: manual
  title: 'ctdR: Enrichment Analysis of Chemical-Gene Interactions from the Comparative
    Toxicogenomics Database'
  authors:
  - family-names: Corsaro
    given-names: Luigi
    orcid: https://orcid.org/0000-0003-1218-230X
    email: lcorsaro69@gmail.com
  year: '2026'
  notes: R package version 0.99.11
  url: https://github.com/drake69/ctdR
  doi: 10.5281/zenodo.19344200
repository: https://bioc.r-universe.dev
repository-code: https://github.com/drake69/ctdR
commit: 57961d56c89dda51cec7c8dcc4c91ed89f454aa2
url: https://luigicorsaro.com/ctdR/
date-released: '2026-10-04'
contact:
- family-names: Corsaro
  given-names: Luigi
  email: lcorsaro69@gmail.com
  orcid: https://orcid.org/0000-0003-1218-230X
references:
- type: article
  title: 'Comparative Toxicogenomics Database (CTD): update 2023'
  authors:
  - family-names: Davis
    given-names: Allan P
  - family-names: Wiegers
    given-names: Tanya C
  - family-names: Johnson
    given-names: Robin J
  - family-names: Sciaky
    given-names: Daniela
  - family-names: Wiegers
    given-names: Jolene
  - family-names: Mattingly
    given-names: Carolyn J
  journal: Nucleic Acids Research
  year: '2023'
  volume: '51'
  issue: D1
  doi: 10.1093/nar/gkac833
  start: D1257
  end: D1262