CalicoST is a great package for inferring spatial CNAs. However, I came to an issue when I try to provide normal spots when jointly running multiple slides. The documentation of normal reference file: normalidx_file: str, optional The path to the file containing the indices of normal spots in the spatial transcriptomics data. Each line is a single index without header.
I am assuming the index means barcode, but barcodes are often used repeatedly across different slices. There are also no option to specify which slice the index are from. I wonder if CalicoST supports providing normal spots when jointly running multiple slices.
Thanks,
James
CalicoST is a great package for inferring spatial CNAs. However, I came to an issue when I try to provide normal spots when jointly running multiple slides. The documentation of normal reference file:
normalidx_file: str, optional The path to the file containing the indices of normal spots in the spatial transcriptomics data. Each line is a single index without header.I am assuming the index means barcode, but barcodes are often used repeatedly across different slices. There are also no option to specify which slice the index are from. I wonder if CalicoST supports providing normal spots when jointly running multiple slices.
Thanks,
James