├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── SpotClean-package.R ├── calculate_contamination_score.R ├── convert_to_seurat.R ├── create_slide.R ├── decontamination.R ├── keep_high_gene.R ├── mbrain_raw.R ├── read10x.R ├── visualize_heatmap.R ├── visualize_label.R └── visualize_slide.R ├── README.md ├── data └── mbrain_raw.rda ├── inst ├── CITATION └── extdata │ └── V1_Adult_Mouse_Brain_spatial │ ├── scalefactors_json.json │ ├── tissue_lowres_image.png │ └── tissue_positions_list.csv ├── man ├── ARCScore.Rd ├── ConvertToSeurat.Rd ├── CreateSlide.Rd ├── KeepHighGene.Rd ├── Read10x.Rd ├── SpotClean-package.Rd ├── SpotClean.Rd ├── VisualizeHeatmap.Rd ├── VisualizeLabel.Rd ├── VisualizeSlide.Rd └── mbrain_raw.Rd ├── tests ├── spelling.R ├── testthat.R └── testthat │ ├── test-calculate_contamination_score.R │ ├── test-convert_to_seurat.R │ ├── test-create_slide.R │ ├── test-decontamination.R │ ├── test-external_data.R │ ├── test-keep_high_gene.R │ ├── 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