JBreunig

Thanks for the suggestion! I tried that and ended up with the following error: > > runSCENIC_1_coexNetwork2modules(scenicOptions) > 17:14 Creating TF modules > Error in quantile.default(linkList$weight, probs = c(0.75, 0.9))...

I moved on to a scanpy-->pyscenic workflow. I don't believe that I ever got things to work going from pySCENIC to SCENIC but that was before the tutorials were written.

I use spyder. But for that particular step, I just go back to the CLI and run it as a typical linux command (from the appropriate directory). > pyscenic grn...

It looks like: dask - 1.0.0, distributed - 1.28.1, pandas - 0.25.3, msgpack - 0.6.1 and tornado 6.0.3

No, I haven't seen those errors. I did have to play with the num_workers argument but those warning were different. I adjusted my code from this: https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Integration%20with%20scanpy.ipynb But I've now...

The particular step "add_scenic_metadata(adata, auc_mtx, regulons)" is only adding the metadata to the anndata structure. The loom output is farther down (export2loom) but I don't think that's the issue here....

No worries...happy to give what little assistance I can offer ;) Unfortunately, I haven't had time to troubleshoot that function. I tried once it didn't include the features that I...

I'm mainly looking at my data in Scanpy. An alternate way I was going to try to make the loom was to start at [65] in this notebook: https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.ipynb I...