tcpl: the ToxCast pipeline for high-throughput screening data

Bioinformatics. 2017 Feb 15;33(4):618-620. doi: 10.1093/bioinformatics/btw680.


Motivation: 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.

Availability and implementation: tcpl is freely available on the Comprehensive R Archive Network under the GPL-2 license.


MeSH terms

  • Algorithms
  • Computer Simulation
  • Dose-Response Relationship, Drug
  • Drug Evaluation, Preclinical / methods*
  • High-Throughput Screening Assays / methods*
  • Models, Biological*
  • Software*
  • Toxicity Tests / methods*