yq-wang / scbsp Goto Github PK

Hey, I'm trying to run scBSP and it gives a memory error (actually, it simply kills the terminal) using Visium HD data (600k bins/spots)

>>> p_values = scbsp.granp(input_sp_mat, input_exp_mat_raw, d1, d2)
Killed

Adata shape:

AnnData object with n_obs × n_vars = 605471 × 18085
obs: 'in_tissue', 'array_row', 'array_col'
var: 'gene_ids', 'feature_types', 'genome'
uns: 'spatial'
obsm: 'spatial'

Unfortunately, it doesn't seem to be compatible with high resolution spatial data

Thanks