Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object


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Documentation for package ‘SpatialExperimentIO’ version 1.0.0

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.sanityCheck Sanity check if one and only file with the specified name pattern exists in the data download directory, and return the file path to .csv Used for count matrix and metadata only, as they require unique.
addParquetPathsCosmx Add CosMx-related parquet paths to metadata for transcripts, polygon, or cell/nucleus boundaries.
addParquetPathsXenium Add Xenium-related parquet paths to metadata for transcripts or cell/nucleus boundaries.
addParquetPathToMeta Add parquet paths to metadata for transcripts, polygon, or cell/nucleus boundaries.
csvToParquetPaths If transcripts or polygon is expected to be loaded, write a parquet file to the current data download (if not already), and return the file path to .parquet
readCosmxSXE Load data from a Nanostring CosMx experiment
readMerscopeSXE Load data from a Vizgen MERSCOPE experiment
readSeqfishSXE Load data from a Spatial Genomics seqFISH experiment
readStarmapplusSXE Load data from a STARmap PLUS experiment
readXeniumSXE Load data from a 10x Geonomics Xenium experiment