BSA

The goal of BSA is to reimplement Daniel’s BSA2 code in a package structure such that it may be installed using R install. This may also form the seed of either a software or workflow package on bioconductor.

Installation

install.packages("remotes")

remotes::install_github("cmatKhan/BSA")

Usage

The first thing that you will need to do iscreate a samplesheet and process the data through the BSA processing pipeline.

Instructions for creating this samplesheet are in the Article (above) called CreatePipelineSampleSheet.

Next, you will be using the functions in this package to analyze the data. An example of the process are in BSA3 and BSA6.

Citation

Below is the citation output from using citation('BSA') in R. Please run this yourself to check for any updates on how to cite BSA.

print(citation('BSA'), bibtex = TRUE)
#> To cite package 'BSA' in publications use:
#> 
#>   Agustihno, Daniel (2023). "Daniel's paper placeholder." _bioRxiv_. ,
#>   <https://www.biorxiv.org/content/10.1101/TODO>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Daniel's paper placeholder},
#>     author = {{Agustihno} and {Daniel}},
#>     year = {2023},
#>     journal = {bioRxiv},
#>     doi = {10.1101/TODO},
#>     url = {https://www.biorxiv.org/content/10.1101/TODO},
#>   }

Please note that the BSA 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 BSA project is released with a Contributor 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 through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The code is styled automatically thanks to styler.
The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.