https://github.com/lieberinstitute/jaffelab
R package with commonly used functions by the Jaffe lab
https://github.com/lieberinstitute/jaffelab
libd rnaseq rstats
Last synced: 5 months ago
JSON representation
R package with commonly used functions by the Jaffe lab
- Host: GitHub
- URL: https://github.com/lieberinstitute/jaffelab
- Owner: LieberInstitute
- Created: 2016-10-05T15:38:03.000Z (about 9 years ago)
- Default Branch: devel
- Last Pushed: 2024-12-12T22:08:19.000Z (10 months ago)
- Last Synced: 2025-03-31T07:22:06.021Z (6 months ago)
- Topics: libd, rnaseq, rstats
- Language: R
- Homepage: http://lieberinstitute.github.io/jaffelab
- Size: 3.68 MB
- Stars: 7
- Watchers: 11
- Forks: 3
- Open Issues: 4
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# jaffelab
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://codecov.io/gh/LieberInstitute/jaffelab?branch=devel)
[](https://github.com/LieberInstitute/jaffelab/actions/workflows/check-bioc.yml)
[](https://github.com/LieberInstitute/jaffelab/issues)
[](https://github.com/LieberInstitute/jaffelab/pulls)
[](https://zenodo.org/badge/latestdoi/70074284)
`jaffelab` is a package initially developed by Andrew E Jaffe's team at the Lieber Institute for Brain Development. It contains several helper functions used in their analyses.
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `jaffelab` using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("LieberInstitute/jaffelab")
```
## Citation
Below is the citation output from using `citation('jaffelab')` in R. Please
run this yourself to check for any updates on how to cite __jaffelab__.
```{r 'citation', eval = requireNamespace('jaffelab')}
print(citation("jaffelab"), bibtex = TRUE)
```
Please note that the `jaffelab` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
## Code of Conduct
Please note that the `jaffelab` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
## Development tools
* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://LieberInstitute.github.io/jaffelab) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.