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ToxCast Data Pipeline Overview

posted on 2019-03-27, 14:29 authored by EPA's National Center for Computational Toxicology
The tcpl package was developed to process high-throughput and high-content screening data generated by the ToxCast program. ToxCast is screening thousands of chemicals with hundreds of assays coming from numerous and diverse biochemical and cell-based technology platforms. The diverse data, received in heterogeneous formats from numerous vendors, are transformed to a standard computable format and loaded into the tcpl database by vendor-specific R scripts. Once data is loaded into the database, ToxCast utilizes the generalized processing functions provided in this package to process, normalize, model, qualify, flag, inspect, and visualize the data. While developed primarily for ToxCast, we have attempted to make the tcpl package generally applicable to chemical-screening community.