Sijie Chen

> Thank you for your reply! Sorry for my delay in getting back to this. I have tried a number of ways to modify this, including your suggestion. I believe...

Thank you Xiaojie. It has been fixed.

I suggest removing dask from pyscenic. It brings much more difficulties than efficiency boosts.

I also met TF missing problems, so I may take my chance on these chipseq-derived databases right? encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__10kb_up_and_down_tss.max encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__500bp_up_and_100bp_down_tss.max I always used these two files on my human data: hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr,...

> thank you. it seems that the ncbi api changed.

thanks for your quick response It is not empty

For your information, I deleted the umap embedding and recomputed umap with `dyn.tl.reduceDimension(adata2,kwargs={'min_dist':0.01},enforce=True)` only to find it yields exactly the same umap  The default min_dist=0.5 in dynamo https://github.com/aristoteleo/dynamo-release/blob/1d1f5c521d0b8763ab866dcc3c3d96be0ba3f8f3/dynamo/tools/utils_reduceDimension.py#L203, The...

Ohh I think I might have found the reason- `min_dist` should be the solution! I was not supposed to pass the min_dist parameter in this way `dyn.tl.reduceDimension(adata2,kwargs={'min_dist':0.01},enforce=True)` It should be...

same problem, it could not be used in pyscenic which requires loompy v3

The same requirement. Can you please publish a win wrapper?