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tcpl: The ToxCast Pipeline for High-Throughput Screening Data
Citation:
Filer, Dayne L., P. Kothiya, R. Woodrow Setzer, Richard S. Judson, AND Matthew T. Martin. tcpl: The ToxCast Pipeline for High-Throughput Screening Data. BIOINFORMATICS. Oxford University Press, Cary, NC, , 1-3, (2016).
Impact/Purpose:
The tcpl R package and its associated MySQL database provide a generalized platform for efficiently storing, normalizing, and dose-response modeling of 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.
Description:
Motivation: The large and diverse high-throughput chemical screening efforts carried out by the US EPAToxCast program requires an efficient, transparent, and reproducible data pipeline.Summary: The tcpl R package and its associated MySQL database provide a generalized platform forefficiently storing, normalizing, and dose-response modeling of high-throughput and high-content chemicalscreening data. The novel dose-response modeling algorithm has been tested against millions of diversedose-response series, and robustly fits data with outliers and cytotoxicity-related signal loss.Availability: The tcpl package is freely available on the Comprehensive R Archive Network under theGPL-2 license.
URLs/Downloads:
http://bioinformatics.oxfordjournals.org/content/early/2016/10/25/bioinformatics.btw680