Advice regarding complex multimodal integration/analysis strategy

Hi all,

I have a couple of human cancer types, each with different modalities (scRNAseq,CITEseq,MERFISH for cancer type #1 and scRNAseq,CITEseq,scATACseq,multiome for cancer type #2), some have different technology versions (10x scRNAseq 3’ V2/V3 or 5’). I’m interested in leveraging the multiome as dictionary to map between the ‘unpaired’ RNA to ATAC, and the RNA across cancer types to map the MERFISH imaging across all of these samples.

What’s the best course of action to implement this? I see the separate tutorials for each separate task, but it’s not clear how they would fit together, especially with the imaging (i.e. how can I have for a cell from cancer type 2 the state or prediction of RNA, ATAC, and spatial relationships?).