The tcplfit2 R package performs basic concentration-response curve fitting. The original tcplFit() function in the ToxCast Data Analysis Pipeline (tcpl) R package performed basic concentration-response curvefitting to 3 models. With tcplfit2, the core tcpl concentration-response functionality has been expanded to process diverse high-throughput screen (HTS) data generated at the US Environmental Protection Agency, including targeted ToxCast, high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP).
tcplfit2 can be used independently to support analysis for diverse chemical screening efforts. tcplfit2 v0.1.7 as a dependency in tcpl v3.2.0 was used to process data in invitrodb v4.2. ToxCast’s invitrodb v4.2 (September 2024) is available for download here: https://www.epa.gov/chemical-research/exploring-toxcast-data.
Updates
- 🚀 Biphasic Polynomial 2 Model Updates #82
- 🚀 Benchmark Dose (BMD) Bounding #52 #48 #54 #72
- 🚀 Plotting Capabilities #77
- 🧪 Area Under the Curve (AUC) Calculation #19 #40 #35 #64 #64
- 🐞Error model distribution argument #41 #42 #84
- 🐞Hitcalling toplikelihood correction for negative responses #89
- 📄 Vignette updates #51 #65 #87 #95 #102
- 📄General package documentation updates #27 #67 #45
- 🛠️ Unit tests #39 #47 #73 #74 #75 #76 #78 #79
Full Changelog: v0.1.6...v0.1.7
Contributors
@brown-jason @sedavid01 @gracezhihuizhao @madison-feshuk @kpaulfriedman
New Contributors
- @sedavid01 made their first contribution in #82
Emoji Legend
🚀 Feature - this is a new feature or improvement to the existing application
🧪 In Progress - a feature actively under development; may not yet be available in production
🐞 Bug - fixed an error in the current software
📄 Documentation - updated user/developer documentation
🔒 Security Updates - security related updates
🛠️ Developer Tools - updated internal tooling for a better developer experience
