SpatialDM

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Memory limit during sdm.spatialdm_local

1

Hello, I'm using stereo-seq with lower bin size, and so I've got a few ten thousands of pixels, when I try to run spatialdm_local it tells me my memory is...

Jiayi-Zheng

Hello, I noticed that the package compares the actual global I with the permuted global I's to compute the permutation p-value: adata.uns['global_stat']['perm']['global_p'] = 1 - (adata.uns['global_I'] \ > adata.uns['global_stat']['perm']['global_perm'].T).sum(axis=0) /...

sealx017

AttributeError: 'csr_matrix' object has no attribute 'A'

1

I'm trying to run the tutorial and am receiving this error while running sdm.spatialdm_local(adata, n_perm=1000, method='both', specified_ind=None, nproc=1). The full error is pasted below: Traceback (most recent call last): File...

moor2562

Hi, Thanks for the amazing tool! Is it possible that after running everything, to extract top K most likely sender-receiver cell-type pair for a specific ligand-receptor pathway? Thanks!

HarryZhang1224

planning for upgrading in the next 10 days

1

Some draft tasks, please keep adding: - [ ] the selection of l value for the spatial weight matrix (needs to be more automated & more intuitive instructions - [...

huangyh09