# SpotClean adjusts for spot swapping in spatial transcriptomics data

## Documentation for package ‘SpotClean’ version 1.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SpotClean-package | SpotClean: a computational method to adjust for spot swapping in spatial transcriptomics data
arcScore | Calculate the ambient RNA contamination (ARC) score
arcScore.default | Calculate the ambient RNA contamination (ARC) score
arcScore.SummarizedExperiment | Calculate the ambient RNA contamination (ARC) score
convertToSeurat | Convert slide object to Seurat object
createSlide | Create a new slide object
keepHighGene | Filter and return highly expressed or highly variable genes
mbrain_raw | Example 10x Visium spatial data: raw count matrix
read10xRaw | Read 10x Space Ranger output data
read10xRawH5 | Read 10x Space Ranger output data
read10xSlide | Read 10x Space Ranger output data
SpotClean | SpotClean: a computational method to adjust for spot swapping in spatial transcriptomics data
spotclean | Decontaminate spot swapping effect in spatial transcriptomics data
spotclean.SpatialExperiment | Decontaminate spot swapping effect in spatial transcriptomics data
spotclean.SummarizedExperiment | Decontaminate spot swapping effect in spatial transcriptomics data
visualizeHeatmap | Visualize spot values on the 2D slide
visualizeHeatmap.default | Visualize spot values on the 2D slide
visualizeHeatmap.SummarizedExperiment | Visualize spot values on the 2D slide
visualizeLabel | Visualize spot labels on the 2D slide
visualizeLabel.default | Visualize spot labels on the 2D slide
visualizeLabel.SummarizedExperiment | Visualize spot labels on the 2D slide
visualizeSlide | Visualize the Visium slide image