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 any issues using the package or would like to make a suggestion, 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')
andBiocStyle::CRANpkg('roxygen2')
.
This package was developed using BiocStyle::Biocpkg('biocthis')
.