tcplfit2: an R-language general purpose concentration-response modeling package.

Abstract

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. tcplfit2 is written in R and is available from CRAN.