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dmcable / spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
GNU General Public License v3.0
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Run RCTD with 10x visium #6

Closed r-melo closed 4 years ago

r-melo commented 4 years ago

Hi,

Is it possible to run RCTD with 10 visium spatial transcriptomics instead of slideseq? In that case how should I change or adapt function read.SpatialRNA?

Thank you

dmcable commented 4 years ago

Yes, the function read.SpatialRNA reads in a dge matrix and coordinates matrix, both of which can be obtained from a Visium dataset.

r-melo commented 4 years ago

Thanks!