I have a question about how raw sequencing data from spatial transcriptomics platforms should be processed before running SpiceMix. The SpiceMix tutorial(spatialLIBD) uses a CSV file with columns named "gene", "spot", and "count" as input data, but this does not reflect real-world spatial transcriptomics data.
For example, could you provide an example showing how to take space ranger outputs and process it into the "gene", "spot", and "count" matrix needed as input for SpiceMix? A walkthrough of this preprocessing step would help make SpiceMix more accessible to researchers analyzing real spatial omics data. Thanks.
I have a question about how raw sequencing data from spatial transcriptomics platforms should be processed before running SpiceMix. The SpiceMix tutorial(spatialLIBD) uses a CSV file with columns named "gene", "spot", and "count" as input data, but this does not reflect real-world spatial transcriptomics data.
For example, could you provide an example showing how to take space ranger outputs and process it into the "gene", "spot", and "count" matrix needed as input for SpiceMix? A walkthrough of this preprocessing step would help make SpiceMix more accessible to researchers analyzing real spatial omics data. Thanks.