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r-tcpl

US EPA's Toxicity Forecaster (ToxCast) Pipeline. More information on the ToxCast program available here: https://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast

https://github.com/usepa/comptox-toxcast-tcpl

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 29 committers (3.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.9%) to scientific vocabulary

Keywords

ccte comptox ord
Last synced: 6 months ago · JSON representation

Repository

US EPA's Toxicity Forecaster (ToxCast) Pipeline. More information on the ToxCast program available here: https://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast

Basic Info
Statistics
  • Stars: 38
  • Watchers: 12
  • Forks: 20
  • Open Issues: 30
  • Releases: 3
Topics
ccte comptox ord
Created almost 9 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# tcpl: The ToxCast Data Analysis Pipeline Supporting Accessible Bioactivity Data for Toxicology



[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/tcpl)](https://cran.r-project.org/package=tcpl)
[![Active](http://img.shields.io/badge/Status-Active-green.svg)](https://cran.r-project.org/package=tcpl) 
[![Monthly Downloads](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)
[![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/tcpl)](https://cran.r-project.org/package=tcpl)
[![DOI](https://zenodo.org/badge/doi/	10.32614/CRAN.package.tcpl.svg)](http://dx.doi.org/10.32614/CRAN.package.tcpl)
[![R-CMD-check](https://github.com/USEPA/CompTox-ToxCast-tcpl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/USEPA/CompTox-ToxCast-tcpl/actions/workflows/R-CMD-check.yaml)


## Welcome to the GitHub repository for the tcpl package.



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](https://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast). tcpl can be used to support diverse chemical screening efforts.

If you are interested in contributing or want to report a bug, please submit a issue or start a discussion. See [CONTRIBUTING](https://github.com/USEPA/CompTox-ToxCast-tcpl/blob/dev/CONTRIBUTING.md) for more information. 

To install the current development version, run the following command: 

    devtools::install_github("USEPA/CompTox-ToxCast-tcpl")
    
### Disclaimer

The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.

Owner

  • Name: U.S. Environmental Protection Agency
  • Login: USEPA
  • Kind: organization
  • Location: United States of America

GitHub Events

Total
  • Fork event: 8
  • Create event: 33
  • Release event: 1
  • Issues event: 71
  • Watch event: 9
  • Delete event: 8
  • Member event: 2
  • Issue comment event: 54
  • Push event: 123
  • Gollum event: 2
  • Pull request review comment event: 39
  • Pull request review event: 75
  • Pull request event: 59
Last Year
  • Fork event: 8
  • Create event: 33
  • Release event: 1
  • Issues event: 71
  • Watch event: 9
  • Delete event: 8
  • Member event: 2
  • Issue comment event: 54
  • Push event: 123
  • Gollum event: 2
  • Pull request review comment event: 39
  • Pull request review event: 75
  • Pull request event: 59

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 781
  • Total Committers: 29
  • Avg Commits per committer: 26.931
  • Development Distribution Score (DDS): 0.697
Past Year
  • Commits: 241
  • Committers: 10
  • Avg Commits per committer: 24.1
  • Development Distribution Score (DDS): 0.564
Top Committers
Name Email Commits
jbrown20 b****n@e****v 237
cthunes t****r@e****v 105
Dunham D****t@e****v 70
Todd Zurlinden z****d@e****v 60
Sarah Davidson d****e@e****v 55
Madison Feshuk f****n@e****v 39
Katie Paul-Friedman p****e@e****v 34
Dayne d****r@g****m 30
spendse s****e@s****m 29
brown-jason 4****n 20
Ko K****y@e****v 18
Kolaczkowski K****i@e****v 17
Michael B. Black m****k@s****m 11
mshobair s****d@e****v 10
tjzurlin t****n@g****m 10
Patrick McMullen p****n@s****m 7
SWatford w****n@e****v 6
Thunes T****r@e****v 4
Carter Thunes 1****s 4
nrush r****l@e****v 3
Kurt Dunham 1****m 2
tzurlind t****n@r****u 2
spendse s****e@g****m 2
Eric Dean Watt e****t@g****m 1
Martin M****t@e****v 1
swatford s****d 1
Julia Ortiz o****a@e****v 1
Bastian Selman 4****1 1
Watford W****n@e****v 1
Committer Domains (Top 20 + Academic)
epa.gov: 16 scitovation.com: 3 rams.colostate.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 205
  • Total pull requests: 171
  • Average time to close issues: 4 months
  • Average time to close pull requests: 21 days
  • Total issue authors: 17
  • Total pull request authors: 11
  • Average comments per issue: 0.83
  • Average comments per pull request: 0.7
  • Merged pull requests: 152
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 42
  • Pull requests: 62
  • Average time to close issues: 29 days
  • Average time to close pull requests: 12 days
  • Issue authors: 3
  • Pull request authors: 6
  • Average comments per issue: 0.36
  • Average comments per pull request: 0.74
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • madison-feshuk (85)
  • brown-jason (53)
  • cthunes (29)
  • kpaulfriedman (10)
  • ldecicco-USGS (5)
  • Kelly-Carstens-EPA (4)
  • kurtdunham (2)
  • paulsonak (2)
  • Ashley-Ko (2)
  • tcrombie (1)
  • bselman1 (1)
  • sedavid01 (1)
  • cmball1 (1)
  • daynefiler (1)
  • t-anton (1)
Pull Request Authors
  • cthunes (105)
  • brown-jason (49)
  • madison-feshuk (18)
  • Ashley-Ko (10)
  • ElizabethGilson (9)
  • kurtdunham (4)
  • jabedini-2404 (4)
  • HendricksJudy (2)
  • knuppla (2)
  • gracezhihuizhao (2)
  • Kelly-Carstens-EPA (2)
  • bselman1 (1)
Top Labels
Issue Labels
enhancement (52) bug (47) documentation (13) invalid (3) question (1) help wanted (1)
Pull Request Labels
enhancement (46) bug (36) documentation (14) invalid (6)

Packages

  • Total packages: 2
  • Total downloads:
    • cran 983 last-month
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 17
  • Total maintainers: 1
cran.r-project.org: tcpl

ToxCast Data Analysis Pipeline

  • Versions: 13
  • Dependent Packages: 2
  • Dependent Repositories: 2
  • Downloads: 983 Last month
Rankings
Forks count: 5.8%
Stargazers count: 11.6%
Average: 12.7%
Downloads: 13.1%
Dependent packages count: 13.2%
Dependent repos count: 19.5%
Maintainers (1)
brown.jason@epa.gov
Last synced: 6 months ago
conda-forge.org: r-tcpl
  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Forks count: 40.0%
Average: 42.9%
Stargazers count: 46.3%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • DBI * imports
  • RColorBrewer * imports
  • RMariaDB * imports
  • data.table >= 1.9.4 imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • numDeriv * imports
  • sqldf * imports
  • stats * imports
  • utils * imports
  • htmlTable * suggests
  • knitr * suggests
  • prettydoc * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat >= 2.1.0 suggests
.github/workflows/test-on-PR.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite