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The CTDquerier R/Bioconductor package allows users to query CTD by gene, by chemical and by disease using single or multiple terms. The terms are validated against the CTD vocabulary used to download the multiple results from CTD as TSV files. The TSV files are read as DataFrames and once encapsulated in an S4 object of class CTDdata. Three methods are provided for CTDdata objects: (i) get_terms retrieves the terms that are validated in CTD vocabulary files; (ii) get_table fetches data from CTD as an object of class DataFrame; and (iii) enrich performs a Fisher’s exact test between two CTDdata objects.


This project published an R package in Bioconductor:

And with a publication in Bioinformatics (Open Access):

CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies.

Carles Hernandez-Ferrer and Juan R. Gonzalez / Bioinformatics 2018 / doi:10.1093/bioinformatics/bty326

Carles Hernandez-Ferrer

Carles Hernandez-Ferrer

Bioinformatics, data analysis and software development

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