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tcpl: the ToxCast pipeline for high-throughput screening data.

Publication ,  Journal Article
Filer, DL; Kothiya, P; Setzer, RW; Judson, RS; Martin, MT
Published in: Bioinformatics (Oxford, England)
February 2017
Published version (DOI)

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.tcpl is freely available on the Comprehensive R Archive Network under the GPL-2 license.martin.matt@epa.gov.

Duke Scholars

Dayne Filer
Author Dayne Filer  

Published In

Bioinformatics (Oxford, England)

DOI

10.1093/bioinformatics/btw680

EISSN

1367-4811

ISSN

1367-4803

Publication Date

February 2017

Volume

33

Issue

4

Start / End Page

618 / 620

Related Subject Headings

  • Toxicity Tests
  • Software
  • Models, Biological
  • High-Throughput Screening Assays
  • Drug Evaluation, Preclinical
  • Dose-Response Relationship, Drug
  • Computer Simulation
  • Bioinformatics
  • Algorithms
  • 49 Mathematical sciences
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Filer, D. L., Kothiya, P., Setzer, R. W., Judson, R. S., & Martin, M. T. (2017). tcpl: the ToxCast pipeline for high-throughput screening data. Bioinformatics (Oxford, England), 33(4), 618–620. https://doi.org/10.1093/bioinformatics/btw680
Filer, Dayne L., Parth Kothiya, R Woodrow Setzer, Richard S. Judson, and Matthew T. Martin. “tcpl: the ToxCast pipeline for high-throughput screening data.” Bioinformatics (Oxford, England) 33, no. 4 (February 2017): 618–20. https://doi.org/10.1093/bioinformatics/btw680.
Filer DL, Kothiya P, Setzer RW, Judson RS, Martin MT. tcpl: the ToxCast pipeline for high-throughput screening data. Bioinformatics (Oxford, England). 2017 Feb;33(4):618–20.
Filer, Dayne L., et al. “tcpl: the ToxCast pipeline for high-throughput screening data.” Bioinformatics (Oxford, England), vol. 33, no. 4, Feb. 2017, pp. 618–20. Epmc, doi:10.1093/bioinformatics/btw680.
Filer DL, Kothiya P, Setzer RW, Judson RS, Martin MT. tcpl: the ToxCast pipeline for high-throughput screening data. Bioinformatics (Oxford, England). 2017 Feb;33(4):618–620.

Published In

Bioinformatics (Oxford, England)

DOI

10.1093/bioinformatics/btw680

EISSN

1367-4811

ISSN

1367-4803

Publication Date

February 2017

Volume

33

Issue

4

Start / End Page

618 / 620

Related Subject Headings

  • Toxicity Tests
  • Software
  • Models, Biological
  • High-Throughput Screening Assays
  • Drug Evaluation, Preclinical
  • Dose-Response Relationship, Drug
  • Computer Simulation
  • Bioinformatics
  • Algorithms
  • 49 Mathematical sciences