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tcpl: the ToxCast pipeline for high-throughput screening data
Abstract
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.
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Cited by
Thomas, R. S., Bahadori, T., Buckley, T. J., Cowden, J., Deisenroth, C., Dionisio, K. L., Frithsen, J. B., Grulke, C. M., Gwinn, M. R., Harrill, J. A., et al. (2019) · Toxicological Sciences · doi:10.1093/toxsci/kfz058 · Cited by 373
Self-citationThe Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology
Richard, A. M., Huang, R., Waidyanatha, S., Shinn, P., Collins, B. J., Thillainadarajah, I., Grulke, C. M., Williams, A. J., Lougee, R. R., Judson, R. S., et al. (2021) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.0c00264 · Cited by 323
Self-citationCiallella, H. L., & Zhu, H. (2019) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.8b00393 · Cited by 227
Nyffeler, J., Willis, C., Lougee, R., Richard, A., Paul-Friedman, K., & Harrill, J. A. (2020) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2019.114876 · Cited by 136
Escher, B. I., Henneberger, L., König, M., Schlichting, R., & Fischer, F. C. (2020) · Environmental Health Perspectives · doi:10.1289/ehp6664 · Cited by 123
Metadata
- Authors
- Filer, D. L., Kothiya, P., Setzer, R. W., Judson, R. S., & Martin, M. T.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-11-22
- Volume
- 33
- Issue
- 4
- Pages
- 618-620
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2546044736
- Cited by
- 230
- References
- 0
- FWCI
- 17.86
- Type
- journal article
- Language
- en
- Open access
- closed
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- 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. https://doi.org/10.1093/bioinformatics/btw680
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