delegate's Introduction

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.

Contributors

Stargazers

Watchers

delegate's Issues

Error in get_data when meta data is tibble

Ensure vector output here

https://github.com/cancerbits/DElegate/blob/9f6b99c0d5949331757b4ab6872dd8e9dc7854f2/R/de_utilities.R#L230C15-L230C15

need to add drop = TRUE in case of tibble input

Method used to make the pseudoreplicates

Hello,

I don't know if I missed it in the article or in the vignette but I'm wondering exactly how the pseudo replicates are made, in particular, when using a seurat object.

Thank you for your work.

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