running C-SIDE to find DE for one cell type between different tissues

dmcable / spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

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running C-SIDE to find DE for one cell type between different tissues #187

Closed LooLipin closed 10 months ago

LooLipin commented 10 months ago

Thanks for the package! I was wondering if it is possible to run C-SIDE on the same cell types across different tissues, ie early stage vs late stage tumors to find genes that are differentially expressed?

From my understanding, the current pipeline only does DE of one cell type vs others in one puck, can we do this for the same cell type but across different pucks?

Best, Lipin

LooLipin commented 10 months ago

Apologies, I found a new vignette for the replicates analysis so I will close this issue.