Releases: USEPA/CompTox-ToxCast-tcpl
v3.2.0
The ToxCast Data Analysis Pipeline (tcpl) is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, invitrodb. The package was developed for the chemical screening data generated by the US EPA’s Toxicity Forecaster (ToxCast) program. tcpl can be used to support diverse chemical screening efforts.
tcpl v3.2.0, along with the dependency package tcplfit2 v0.1.7, 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
- 🚀 Integration with the Computational Toxicology and Exposure (CTX) Bioactivity API via the ctxR package #221 #233 #257 #273 #283
- 🚀 Plotting updates #146 #153 #160 #167 #168 #171 #174 #204 #229 #242 #274
- 🚀 Data processing logic improvements #126 #129 #158 #170 #181 #199 #205 #209 #222
- 🚀 Updates related to schema changes and backwards compatibility #135 #139 #173 #205 #209 #214 #222 #225 #262 #277
- 🚀 Methods updates #123 #129 #130 #136 #138 #143 #194 #195 #220 #239 #243 #261
- 🚀 Cytotoxicity Burst #141 #269 #279
- 🚀 Variable Matrices #186 #264
- 🛠️ Unit tests #282
- 📄 Vignette updates #201 #240 #260 #271 #287 #289 #292
- 📄 General package documentation updates #159 #157 #295 #298 #299
Full Changelog: v3.1.0...v3.2.0
Contributors
@brown-jason @cthunes @madison-feshuk @Ashley-Ko @sedavid01 @gracezhihuizhao @Kelly-Carstens-EPA @kpaulfriedman
New Contributors
- @Kelly-Carstens-EPA made their first contribution in #261
- @gracezhihuizhao made their first contribution in #240
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
Contributors
Assets 2
v3.1.0
Released October 6, 2023
The R software, tcpl, is open-source software used to store, manage, curve-fit, and visualize high-throughput bioactivity screening data included in the US EPA ToxCast program. Tcpl is released in versions at the Comprehensive R Archive Network (CRAN) (https://cran.r-project.org/package=tcpl). Vignettes describing an introduction to tcpl and the structure of the ToxCast database, invitrodb; how assays are annotated in invitrodb; data processing; and data retrieval are available for users seeking additional details on the function of tcpl.
Tcpl v3.1.0 was used to create invitrodb v4.1. ToxCast’s invitrodb v4.1 (September 2023) encompasses major database and software updates and is now available for download here: https://www.epa.gov/chemical-research/exploring-toxcast-data. Updates in tcpl v3.1.0 include:
- SC data processing: Updates to normalization given bidirectionality #19 #32
- Method updates: New methods were to support processing needs, including new aggregation, cutoff, and flags. All method descriptions have been reviewed and updated for completeness. #41 #87 #95 #99 #103 #120 #123 #118 #129 #130 #134 #136 #138
- New functionality and other enhancements, including:
- Vignette updates #65 #66 #68 #71 #72 #80 #86 #93 #131
See changelog https://github.com/USEPA/CompTox-ToxCast-tcpl/pulls?page=2&q=is%3Apr+is%3Amerged+sort%3Aupdated-asc+updated%3A%3E2022-09-30+closed%3A%3C2023-10-01 for more details.