SpotClean adjusts for spot swapping in spatial transcriptomics
data
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Documentation for package ‘SpotClean’ version 1.6.1
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 |