SpatialDE
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Teichlab
Test genes for Spatial Variation
Hi @kant @flying-sheep @ostegle @vals @NickEngland , thanks for your contribution to SpatialDE! I'm facing a bug when I run `resid_expr = NaiveDE.regress_out(adata.obs[['total_counts']], norm_expr.T, 'np.log(total_counts)')` . This produces an error...
In execution of spatialDE.run, the follow error occurs: It is verified that scipy has no attribute of arange, maybe it could be range()?
I get the following error running the scanpy spatial transcriptomics tutorial with the following command: ``` counts = pd.DataFrame(adata.X.todense(), columns=adata.var_names, index=adata.obs_names) coord = pd.DataFrame(adata.obsm['spatial'], columns=['x_coord', 'y_coord'], index=adata.obs_names) results = SpatialDE.run(coord,...
Fix #38 with improvements from @Scoott
Input code: %%time counts = pd.DataFrame(adata.X.todense(), columns=adata.var_names, index=adata.obs_names) coord = pd.DataFrame(adata.obsm['spatial'], columns=['x_coord', 'y_coord'], index=adata.obs_names) results = SpatialDE.run(coord, counts) Output error: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) File :3 File...
Hello, First, thanks for this great tool! I am trying to apply it to a somewhat large single cell resolution vizgen dataset of human lung cancer (Vizgen_Human_LungCancer_Patient1) from the MERSCOPE...
Hello! Just wanted to get some advice on what we can do when the `delta_ELBO` never converges. I have been running SpatialDE for over 2 weeks now with 40 CPUs,...
I have a case where a certain gene appears twice in the results table. This is annoying, because in that case I can't merge it back into an AnnData object....
