What is the Spatial Transcriptomics Analysis Pipeline?
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This is a Spatial Transcriptome Analysis pipeline based on spatialdata and scanpy. The input is '.tar' compressed (not '.tar.gz'!) folder(s) from Xenium output. The output is one html file per sample regarding QC and clustering and one .zarr.tar file per sample. If there are more than one sample, an aggregated html report will be generated.