CTDquerier

CTDquerier facilitates extraction, integration, visualization, and enrichment analysis of data from the Comparative Toxicogenomics Database (CTD) to support analysis of chemical-gene and chemical-disease relationships within R/Bioconductor workflows.

Key Features:

• Data Integration: Download and integrate CTD (Comparative Toxicogenomics Database) data into R/Bioconductor analysis pipelines.
• Enrichment Analysis: Perform enrichment analyses at the chemical-gene and chemical-disease levels to generate hypotheses about causal pathways linking chemicals to diseases.
• Visualization Tools: Provide built-in visualization functions for representing CTD-derived chemical-gene and chemical-disease data.

Scientific Applications:

• Chemical–disease etiology (e.g., asthma): Enable investigation of etiological links between environmental chemicals and human diseases such as asthma.
• Toxicology and toxicogenomics: Support toxicology and toxicogenomics studies by mapping chemical interactions with genes and diseases.
• Genomics and epidemiology: Support genomics and epidemiology research through enrichment analyses and integration with R/Bioconductor tools.

Methodology:

Functions extract and download curated CTD data, integrate it into R/Bioconductor objects, perform chemical-gene and chemical-disease enrichment analyses, and generate visualizations, with implementations designed to handle large datasets efficiently.