FastBMD

FastBMD performs rapid benchmark dose–response analysis of transcriptomics data to derive gene- and pathway-level benchmark doses for toxicological and comparative transcriptomic assessment.

Key Features:

• Computationally efficient implementation: Implemented in R and applies the National Toxicology Program's genomic dose‑response modeling approach, with reported runtimes over 60× faster than current leading tools.
• Standardized regulatory methods: Leverages methods established by international regulatory agencies for genomic dose‑response analysis.
• Processing and normalization: Includes processing and normalization of raw gene expression values as part of the analytical pipeline.
• Pathway-level BMD exploration: Produces pathway-level benchmark doses to examine dose‑response relationships at the pathway scale.
• Annotation‑free pipeline: Supports analysis without genome annotation and includes feature sensitivity‑based point‑of‑departure analysis.
• Cross‑species support: Designed to handle transcriptomics data from 13 different species.
• Comprehensive analytical pipeline: Provides end‑to‑end analysis from raw gene expression processing to pathway‑level BMD results.

Scientific Applications:

• Toxicology and toxicity testing: Derivation of gene‑ and pathway‑level benchmark doses for toxicological dose‑response assessment.
• Regulatory benchmark dose analysis: Generation of BMD estimates using methods aligned with international regulatory agency standards.
• Comparative and non‑model organism studies: Dose‑response analysis of transcriptomics data across multiple species, including analyses that do not require genome annotation.

Methodology:

Implemented in R using the National Toxicology Program's genomic dose‑response modeling approach and standardized regulatory methods; includes processing and normalization of raw gene expression values and feature sensitivity‑based point‑of‑departure analysis to produce gene‑ and pathway‑level BMDs.