Dataset Information

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.

ABSTRACT:

Summary

A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams' trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to-date gene annotations. Furthermore, we have implemented extensive data visualizations, on-the-fly data filtering, and a batch-wise analysis workflow. We have also significantly re-engineered the code base to reflect contemporary software engineering practices and streamline future development. The first version of BMDExpress was developed in 2007 to meet an unmet demand for easy-to-use transcriptomic dose-response analysis software. Since its original release, however, transcriptomic platforms, technologies, pathway annotations and quantitative methods for data analysis have undergone a large change necessitating a significant re-development of BMDExpress. To that end, as of 2016, the National Toxicology Program assumed stewardship of BMDExpress. The result is a modernized and updated BMDExpress 2 that addresses the needs of the growing toxicogenomics user community.

Availability and implementation

BMDExpress 2 is available at https://github.com/auerbachs/BMDExpress-2/releases.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Phillips JR

PROVIDER: S-EPMC6513160 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Publications

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.

Phillips Jason R JR Svoboda Daniel L DL Tandon Arpit A Patel Shyam S Sedykh Alex A Mav Deepak D Kuo Byron B Yauk Carole L CL Yang Longlong L Thomas Russell S RS Gift Jeff S JS Davis J Allen JA Olszyk Louis L Merrick B Alex BA Paules Richard S RS Parham Fred F Saddler Trey T Shah Ruchir R RR Auerbach Scott S SS

Bioinformatics (Oxford, England) 20190501 10

<h4>Summary</h4>A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams' trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to ...[more]

PMID: 30329029

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Dataset Information

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.

Summary

Availability and implementation

Supplementary information

Publications

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.

Similar Datasets

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