Data

Tools

Indexes

Applications

Experiments

Open Source Science

biodosetools

A tool to perform all different statistical tests and calculations needed by Biological Dosimetry Laboratories

https://github.com/biodosetools-team/biodosetools

Science Score: 39.0%

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 11 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (20.4%) to scientific vocabulary

Keywords

biological-data dosimetry shiny-app
Last synced: 9 months ago · JSON representation

Repository

A tool to perform all different statistical tests and calculations needed by Biological Dosimetry Laboratories

Basic Info
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 3
  • Open Issues: 2
  • Releases: 8
Topics
biological-data dosimetry shiny-app
Created over 7 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

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


[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/biodosetools)](https://cran.r-project.org/package=biodosetools)
[![lifecycle](https://lifecycle.r-lib.org/articles/figures/lifecycle-stable.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable-1)
[![R-CMD-check](https://github.com/biodosetools-team/biodosetools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/biodosetools-team/biodosetools/actions/workflows/R-CMD-check.yaml)
[![pkgdown Workflow Status](https://github.com/biodosetools-team/biodosetools/workflows/pkgdown/badge.svg)](https://biodosetools-team.github.io/biodosetools/)
[![Codecov test coverage](https://codecov.io/gh/biodosetools-team/biodosetools/branch/master/graph/badge.svg)](https://app.codecov.io/gh/biodosetools-team/biodosetools?branch=master)
[![doi](https://img.shields.io/badge/DOI-10.1080%2F09553002.2023.2176564-blue)](https://doi.org/10.1080/09553002.2023.2176564)


## Overview

Biodose Tools ([Hernández et al. 2023](https://doi.org/10.1080/09553002.2023.2176564)) is an open source project that aims to be a tool to perform all different tests and calculations needed by biological dosimetry laboratories. The app is developed using the [R](https://www.r-project.org/about.html) programming language and [Shiny](https://shiny.rstudio.com/) as a framework to offer an online, easy-to-use solution. Although the intention is to provide the application as a website, all R routines are available as an R package, which can be downloaded for improvement or personal use.

We also aim to clarify and explain the tests used and to propose those considered most appropriate. Each laboratory in its routine work should choose the most suitable method, but the project aims to reach a consensus that will help us in case of mutual assistance or intercomparisons.

The project is initially developed by [RENEB](https://www.reneb.net/) association, but contributions are always welcome.

## Installation

You can install the released version of {biodosetools} from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("biodosetools")
```

Or install the development version from [GitHub](https://github.com/) with:

```r
devtools::install_github("biodosetools-team/biodosetools")
```

## Examples

To run the Biodose Tools app locally, we can run the following command on the R console, which will invoke the Shiny user interface:

```{r run-app, eval=FALSE, include=TRUE}
library(biodosetools)
run_app()
```

Detailed examples using {biodosetools}'s Shiny user interface as well as its R API to perform dose-effect fitting and dose estimation for the dicentric and translocation assays are available on https://biodosetools-team.github.io/documentation/ in the "Using Biodose Tools" chapters.

## Citation

If you use data, results or conclusion from this work, please cite:

> Hernández, A., Endesfelder, D., Einbeck, J., Puig, P., Benadjaoud, M. A., Higueras, M., Ainsbury, E., Gruel, G., Oestreicher, U., Barrios, L., & Barquinero, J. F. (2023). Biodose Tools: an R shiny application for biological dosimetry. International Journal of Radiation Biology, 1-13. https://doi.org/10.1080/09553002.2023.2176564

A BibTeX entry for LaTeX users is:

```bib
@article{BiodoseTools2023,
  author        = {Alfredo Hern{'{a}}ndez and David Endesfelder and Jochen Einbeck and Pedro Puig and Mohamed Amine Benadjaoud and Manuel Higueras and Elizabeth Ainsbury and Ga{"{e}}tan Gruel and Ursula Oestreicher and Leonardo Barrios and Joan Francesc Barquinero},
  title         = {{Biodose Tools: an R shiny application for biological dosimetry}},
  journal       = {International Journal of Radiation Biology},
  pages         = {1-13},
  year          = {2023},
  publisher     = {Taylor & Francis},
  doi           = {10.1080/09553002.2023.2176564},
  note          = {PMID: 36731491},
  URL           = {https://doi.org/10.1080/09553002.2023.2176564},
  eprint        = {https://doi.org/10.1080/09553002.2023.2176564}
}
```

GitHub Events

Total
  • Create event: 5
  • Release event: 1
  • Issues event: 7
  • Delete event: 4
  • Issue comment event: 2
  • Push event: 43
  • Pull request event: 23
  • Fork event: 2
Last Year
  • Create event: 5
  • Release event: 1
  • Issues event: 7
  • Delete event: 4
  • Issue comment event: 2
  • Push event: 43
  • Pull request event: 23
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,132
  • Total Committers: 1
  • Avg Commits per committer: 1,132.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 53
  • Committers: 1
  • Avg Commits per committer: 53.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alfredo Hernández a****s@g****m 1,132

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 29
  • Total pull requests: 21
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 4 minutes
  • Total issue authors: 6
  • Total pull request authors: 3
  • Average comments per issue: 1.07
  • Average comments per pull request: 0.0
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 18
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 minutes
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • aldomann (12)
  • jorgeegm (8)
  • Gaetan-IRSN (5)
  • YjZ77 (2)
  • dendesfelder (1)
  • neliner (1)
Pull Request Authors
  • Francis-88-cell (11)
  • aldomann (7)
  • teunbrand (1)
Top Labels
Issue Labels
enhancement (7) bug (6) UI improvement (4)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 284 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: biodosetools

An R Shiny Application for Biological Dosimetry

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 284 Last month
Rankings
Forks count: 21.9%
Stargazers count: 22.5%
Dependent packages count: 29.8%
Average: 30.8%
Dependent repos count: 35.5%
Downloads: 44.5%
Maintainers (1)
aldomann.designs@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • MASS * imports
  • bsplus * imports
  • cli * imports
  • config * imports
  • dplyr >= 1.0.0 imports
  • ggplot2 * imports
  • golem * imports
  • htmltools * imports
  • magrittr * imports
  • maxLik * imports
  • mixtools * imports
  • msm * imports
  • rhandsontable * imports
  • rlang >= 0.4.0 imports
  • rmarkdown * imports
  • shiny * imports
  • shinyWidgets >= 0.5.0 imports
  • shinydashboard * imports
  • tidyr >= 1.0.0 imports
  • covr * suggests
  • kableExtra * suggests
  • knitr * suggests
  • markdown * suggests
  • pander * suggests
  • testthat >= 3.0.0 suggests
  • tinytex * suggests
  • xtable * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/deploy-shiny.yml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.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
.github/workflows/R-CMD-check-pull-request.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage-pull-request.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite