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.
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")
Application of the scutrboot
package can be found in the
scUTRquant-figures
repository, particularly
in the notebooks used to generate Figures
4
and
5.
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.
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.
This package was developed using biocthis.
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