Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
US Environmental Protection Agency, RTP NC USA.
Bioinformatics. 2022 Jan 27;38(4):1157-1158. doi: 10.1093/bioinformatics/btab779.
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.
许多化学筛选应用都是在浓度或剂量反应模式下进行的,因此有必要提取适当的参数,包括化学物质/测定物对是否具有活性,如果有活性,则需要确定活性出现的浓度。通常,需要使用多种数学模型或曲线形状来测试数据,以评估最佳拟合。为此,有几个商业程序和开源库可供使用。用于管理高通量筛选 (HTS) 浓度反应数据的广泛使用的系统是 tcpl(ToxCast Pipeline)。当前的 tcpl 实现将浓度反应建模代码与 HTS 数据处理的数据管理和数据库方面紧密集成。tcplfit2 是 tcpl 的曲线拟合和命中调用核心的独立版本,它已扩展到包括许多标准曲线类,并使用基准剂量建模。这个包将对 HTS 浓度反应数据(如高通量全基因组转录组学)非常有用。
tcplfit2 是用 R 编写的,可以从 CRAN 获得。