README.md

In mfansler/scutrboot: Single-Cell UTR Bootstrap Tools

scUTRboot

Overview

The scutrboot package provides a collection of statistical tools for the analysis of 3’ UTR isoform usage from scRNA-seq data. In particular, it was developed to accompany the scUTRquant pipeline, working from 3’ UTR isoform-level count data to characterize isoform usage in groups of cells (e.g., clusters, cell types) and test differential usage across group. The “boot”, both refers to the package’s role as the part of the scUTRx suite where the tools are kept and to the bootstrap-based procedures that are core to the statistical framework.

Installation instructions

Get the latest stable R release from CRAN. Then install scutrboot from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

# not available yet
# BiocManager::install("scutrboot")

And the development version from GitHub with:

BiocManager::install("mfansler/scutrboot")

Usage

Application of the scutrboot package can be found in the scUTRquant-figures repository, particularly in the notebooks used to generate Figures 4 and 5.

Citation

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

print(citation('scutrboot'), bibtex = TRUE)
#> 
#> To cite package 'scutrboot' in publications use:
#> 
#>   Mervin Fansler (2021). scutrboot: Single-Cell UTR Bootstrap Tools. R
#>   package version 0.2.2.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {scutrboot: Single-Cell UTR Bootstrap Tools},
#>     author = {Mervin Fansler},
#>     year = {2021},
#>     note = {R package version 0.2.2},
#>   }

Please note that the scutrboot 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 scutrboot 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.

This package was developed using biocthis.

mfansler/scutrboot documentation built on July 1, 2023, 9:17 p.m.