Multi-omics Alignment

[DruncBread]

Hi, @luosc

Thank you for your great work! I have a few questions after reading your paper and tutorial though:

How does CAST align unpaired multi-omics slices?
Do you think it will work on ATAC and RNA alignment?

If I'm using CAST to align an ATAC slice (peak matrix) and an RNA slice (gene expression matrix), which do not have overlapping features, what should I do?

Best regards.

[luosc]

Thank you for your interest. We indeed assume shared feature space as a requirement to use our CAST_Mark module (the GNN model), however, if you have a meaningful embedding or feature that shows correlation across slices with region specificity, you could directly use that for CAST Stack module, this module start with a correlation matrix between cells in space, theoretically if you know a few genes that show strong spatial patterns as a biological prior, that would possibly work too.

[DruncBread]

Hi, @luosc

Thank you very much for your reply and guidance!

I will try converting peak matrix to gene activity score matrix so that the ATAC slice would shared common gene feature with the RNA slice.

Best regards.