Overview
SpatialDryArtifacts implements enhanced methods for detecting edge dryspots - technical artifacts caused by incomplete reagent coverage during Visium spatial transcriptomics sample preparation. This package extends existing spatial transcriptomics quality control methods by incorporating spatial neighborhood information.
Key Features
- Detection of edge dryspots using raster-based focal transformations
- Classification of problem areas into removal categories
- Integration with existing Bioconductor workflows
- Compatibility with SpatialExperiment objects
Installation
You can install the development version of SpatialDryArtifacts from GitHub with:
# install.packages("pak")
pak::pak("CambridgeCat13/SpatialDryArtifacts")Example
This is a basic example which shows you how to solve a common problem:
library(SpatialDryArtifacts)
# Detect edge dryspots
spe <- detectEdgeDryspots(spe, qc_metric = "sum_gene")
# Classify results
spe <- classifyEdgeDryspots(spe)Documentation
Visit the package website: https://cambridgecat13.github.io/SpatialDryArtifacts/