tcpl: the ToxCast pipeline for high-throughput screening data | Zendy

Dayne L. Filer | Zendy; Parth Kothiya | Zendy; R. Woodrow Setzer | Zendy; Richard Judson | Zendy; Matthew T. Martin | Zendy

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tcpl: the ToxCast pipeline for high-throughput screening data

Author(s) -

Dayne L. Filer,

Parth Kothiya,

R. Woodrow Setzer,

Richard Judson,

Matthew T. Martin

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw680

Subject(s) - pipeline (software) , computer science , throughput , outlier , high throughput screening , data mining , license , bioinformatics , artificial intelligence , biology , operating system , wireless

Large high-throughput screening (HTS) efforts are widely used in drug development and chemical toxicity screening. Wide use and integration of these data can benefit from an efficient, transparent and reproducible data pipeline. Summary: The tcpl R package and its associated MySQL database provide a generalized platform for efficiently storing, normalizing and dose-response modeling of large high-throughput and high-content chemical screening data. The novel dose-response modeling algorithm has been tested against millions of diverse dose-response series, and robustly fits data with outliers and cytotoxicity-related signal loss.

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