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FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data.

ABSTRACT:

Motivation

Transcriptomics dose-response analysis is a promising new approach method for toxicity testing. While international regulatory agencies have spent substantial effort establishing a standardized statistical approach, existing software that follows this approach is computationally inefficient and must be locally installed.

Results

FastBMD is a web-based tool that implements standardized methods for transcriptomics benchmark dose-response analysis in R. It is >60 times faster than the current leading software, supports transcriptomics data from 13 species, and offers a comprehensive analytical pipeline that goes from processing and normalization of raw gene expression values to interactive exploration of pathway-level benchmark dose results.

Availability and implementation

FastBMD is freely available at www.fastbmd.ca.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Ewald J

PROVIDER: S-EPMC8128449 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data.

Ewald Jessica J Soufan Othman O Xia Jianguo J Basu Niladri N

Bioinformatics (Oxford, England) 20210501 7

<h4>Motivation</h4>Transcriptomics dose-response analysis is a promising new approach method for toxicity testing. While international regulatory agencies have spent substantial effort establishing a standardized statistical approach, existing software that follows this approach is computationally inefficient and must be locally installed.<h4>Results</h4>FastBMD is a web-based tool that implements standardized methods for transcriptomics benchmark dose-response analysis in R. It is >60 times fas ...[more]

PMID: 32761065

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