Spatially-aware quality control for spatial transcriptomics • SpotSweeper

SpotSweeper is a package developed for spatially-aware quality control (QC) methods for the detection, visualization, and removal of both local outliers and regional artifacts in spot-based spatial transcriptomics data, such as 10x Genomics Visium, using standard QC metrics.

If you experience an issues user the package, please open an issue on the GitHub repository.

To find more information, please visit the documentation website.

Installation instructions

You can install the latest version of SpotSweeper from Bioconductor with the following code:

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

BiocManager::install("SpotSweeper")

The latest development version can be installed from GitHub using the following:

if (!require("devtools")) install.packages("devtools")
remotes::install_github("MicTott/SpotSweeper")

Tutorials

A detailed tutorial is available in the package vignette from Bioconductor. A direct link to the tutorial / package vignette is available here.

Development tools

Continuous code testing is possible thanks to GitHub actions through BiocStyle::Biocpkg('biocthis').
The documentation website is automatically updated thanks to BiocStyle::CRANpkg('pkgdown').
The code is styled automatically thanks to BiocStyle::CRANpkg('styler').
The documentation is formatted thanks to BiocStyle::CRANpkg('devtools') and BiocStyle::CRANpkg('roxygen2').

This package was developed using BiocStyle::Biocpkg('biocthis').