lieberinstitute / visiumstitched

R package containing functions useful for stitching Visium capture areas. Related to https://github.com/LieberInstitute/LS_visiumStitched

visiumStitched

visiumStitched provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/LS_visiumStitched. This packages, among other utilities, it includes a function for plotting several capture areas stitched together.

For details, check the documentation site.

Installation instructions

Get the latest stable R release from CRAN. Then install visiumStitched from GitHub using the following code:

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

BiocManager::install("LieberInstitute/visiumStitched")

Citation

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

print(citation("visiumStitched"), bibtex = TRUE)
#> To cite package 'visiumStitched' in publications use:
#> 
#>   Eagles N (2024). _visiumStitched: Helper package for working with
#>   stitched overlapping Visium capture areas_. R package version 0.99.0.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {visiumStitched: Helper package for working with stitched overlapping Visium capture areas},
#>     author = {Nicholas J. Eagles},
#>     year = {2024},
#>     note = {R package version 0.99.0},
#>   }

Please note that the visiumStitched 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 visiumStitched 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.