AI Article Synopsis
- Chemical screening often involves analyzing concentration or dose-response data to determine if a chemical or assay is active and identifying effective concentrations.
- Multiple mathematical models are tested against the data for optimal fit, with tools like tcpl (ToxCast Pipeline) managing high-throughput screening data effectively.
- Tcplfit2, a standalone R package, enhances curve-fitting and hit-calling for concentration-response modeling and is available on CRAN, making it suitable for various high-throughput data applications.
Article Abstract
Summary: Many applications of chemical screening are performed in concentration or dose-response mode, and it is necessary to extract appropriate parameters, including whether the chemical/assay pair is active and if so, what are concentrations where activity is seen. Typically, multiple mathematical models or curve shapes are tested against the data to assess the best fit. There are several commercial programs used for this purpose as well as open-source libraries. A widely used system for managing high-throughput screening (HTS) concentration-response data is tcpl (ToxCast Pipeline). The current implementation of tcpl has the concentration-response modeling code tightly integrated with the data management and databasing aspects of HTS data processing. Tcplfit2 is a stand-alone version of the curve-fitting and hitcalling core of tcpl that has been extended to include a large number of standard curve classes and to use benchmark dose modeling. This package will be useful for HTS concentration-response data such as high-throughput whole genome transcriptomics.
Availability And Implementation: tcplfit2 is written in R and is available from CRAN.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202035 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btab779 | DOI Listing |
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