├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── AllClasses.R ├── AllGenerics.R ├── SpatialExperiment-assays.R ├── SpatialExperiment-colData.R ├── SpatialExperiment-combine.R ├── SpatialExperiment-methods.R ├── SpatialExperiment-rotate-mirror.R ├── SpatialExperiment.R ├── SpatialImage-utils.R ├── SpatialImage.R ├── Validity.R ├── coerce.R ├── imgData-methods.R ├── imgData-utils.R ├── imgData.R ├── read10xVisium.R ├── readImgData.R ├── show.R └── subset.R ├── README.md ├── inst ├── CITATION ├── NEWS └── extdata │ ├── 10xVisium │ ├── section1 │ │ └── outs │ │ │ ├── raw_feature_bc_matrix │ │ │ ├── barcodes.tsv │ │ │ ├── features.tsv │ │ │ └── matrix.mtx │ │ │ └── spatial │ │ │ ├── scalefactors_json.json │ │ │ ├── tissue_lowres_image.png │ │ │ └── tissue_positions_list.csv │ └── section2 │ │ └── outs │ │ ├── raw_feature_bc_matrix │ │ ├── barcodes.tsv │ │ ├── features.tsv │ │ └── matrix.mtx │ │ └── spatial │ │ ├── scalefactors_json.json │ │ ├── tissue_lowres_image.png │ │ └── tissue_positions_list.csv │ └── README ├── man ├── SpatialExperiment-assays.Rd ├── SpatialExperiment-coercion.Rd ├── SpatialExperiment-colData.Rd ├── SpatialExperiment-combine.Rd ├── SpatialExperiment-methods.Rd ├── SpatialExperiment-misc.Rd ├── SpatialExperiment-rotate-mirror.Rd ├── SpatialExperiment-subset.Rd ├── SpatialExperiment.Rd ├── SpatialImage-class.Rd ├── SpatialImage-misc.Rd ├── imgData-methods.Rd ├── read10xVisium.Rd └── readImgData.Rd ├── tests ├── testthat.R └── testthat │ ├── test_SpatialExperiment-assays.R │ ├── test_SpatialExperiment-cbind.R │ ├── test_SpatialExperiment-coercion.R │ ├── test_SpatialExperiment-colData.R │ ├── test_SpatialExperiment-methods.R │ ├── test_SpatialExperiment-rotate-mirror.R │ ├── test_SpatialExperiment-subset.R │ ├── test_SpatialExperiment-validity.R │ ├── test_SpatialExperiment.R │ ├── test_SpatialImage-methods.R │ ├── test_SpatialImage.R │ ├── test_imgData-methods.R │ 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