Hi all,

I'd like to share ctdR, an R package I've been developing to run enrichment analysis of chemical–gene interactions using data from the Comparative Toxicogenomics Database (CTD).

The idea: given a set of genes of interest (e.g. from a DE analysis), identify the chemicals significantly associated with that gene set — useful for generating hypotheses about environmental exposures, drugs, or toxicants linked to a transcriptional signature.

What it does

It wraps four enrichment methods behind a single interface, so you can switch approach without rewriting your pipeline:

• ORA — via clusterProfiler
• GSEA — via fgsea
• CAMERA — competitive gene-set test, via limma
• GSVA — per-sample enrichment, via GSVA

ORA/GSEA take a gene list; CAMERA/GSVA take an expression matrix.

Typical workflow — two calls:

# Download the CTD chemical–gene interactions file once from ctdbase.org, then:
ctd <- import_CTD("CTD_chem_gene_ixns.tsv.gz")
res <- enrichment_CTD(genes, ctd, method = "ORA")

Notes

• The package does not bundle or redistribute CTD data — you download it yourself and comply with the CTD licensing terms.
• Currently under review for Bioconductor. Apache-2.0.
• Repo, docs and issues: https://github.com/drake69/ctdR

I'd really appreciate feedback from people working with CTD or with chemical/toxicogenomics enrichment: does the four-methods-one-interface approach fit how you'd actually use this? Any method or output you'd expect that's missing?

Thanks!