R Package: canceRbits

Wrapper and helper functions commonly used by the Developmental Cancer Genomics group at St. Anna Children's Cancer Research Institute.

To install from github

To install the latest version

remotes::install_github(repo = 'cancerbits/canceRbits')

For reproducibility, e.g. in a dockerfile, use approaches below

To install a specific version given its tag

remotes::install_github(repo = 'cancerbits/canceRbits', ref = 'v0.1.2')

(All tags are listed here)

To install a specific commit

remotes::install_github(repo = 'cancerbits/canceRbits', ref = '10b959a')

(All commits are listed here)

Workflow for updating the package

• Add/edit one or more .R files in R directory
  • Make sure to include roxygen documentation
• run devtools::document()
• add required packages to NAMESPACE file (if there are new ones)
• (optional) Edit DESCRIPTION file (e.g. add your name, bump the version number)
• (optional) Edit overall package documentation in R/canceRbits.R
• (optional but strongly suggested) Add unit test for new functionality (in tests/testthat/)
• check whether package is still OK via devtools::check(document = FALSE) or via Rstudio menu: 'Build' > 'Check Package'

Conventions

Exported functions have a cb_ prefix in their name.

Suggested reading

R packages by Hadley Wickham and Jenny Bryan

useful cheat sheet

For Seurat v5 add this line to the Rmd script to ensure compatibility

options(Seurat.object.assay.version = 'v3')