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Exploring ToxCast Data: Overview of tcpl R Package

The ToxCast pipeline (tcpl) is an R package that serves as an interface for dose-response modeling and visualization for high-throughput screening efforts based on the data generated by ToxCast. For advanced users who would like to use the tcpl package to process their own data or review the ToxCast data processing, the R package is available for downloadExit. Users will need experience with R to use these files. The R package includes:

  • A reference manual.
  • A vignette describing the package in detail.
  • Exercises to help users work through and understand the vignette.
  • A list of package functions.

The user can choose to use the tcpl package (v2.0) with a MySQL database (Mac version here)Exitor with comma-delimited (*.csv) files that do not require MySQL. A full description of the tcpl configuration options is available in the R manual for tcpl v2.0.

See How to Set up R and MySQL if needed before using.

The package includes the following sections to describe the functionality of the pipeline.

  1. Introduction
  2. Register and Upload New Data
  3. Data Processing and the tcplRun Function
  4. Data Normalization
  5. Single-concentration Screening
    1. Level1
    2. Level2
  6. Multiple-concentration Screening
    1. Level1
    2. Level2
    3. Level3
    4. Level4
    5. Level5
    6. Level6
  7. Field Explanation/Database Structure
    1. Single-concentration tables
    2. Multiple-concentration tables
    3. Auxiliary annotation tables
  8. B Level 0 Pre-processing
  9. C Burst Z-Score Calculation