Reference scRNA

BayesTME can take advantage of reference scRNA data in anndata h5ad format.

This will set a prior on the expression profiles of cell types in the spatial data, it will also consequently set the number of celltypes.

Provide your anndata archive to deconvolve like so:

deconvolve --expression-truth companion_scRNA.h5ad \
    --reference-scrna-celltype-column celltype \
    --reference-scrna-sample-column sample

deconvolve will consider all the samples jointly to determine a prior on celltype expression profiles.

We assume the values of --reference-scrna-celltype-column and --reference-scrna-sample-column are attributes of the obs table in your anndata object.