ctdR

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 'clusterProfiler', 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>).

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• Luigi Corsaro author maintainer