JP Cartailler

Just in case you had missed my delayed response to #3249 (merged above), here was the code used to generate the "overly small font" in win10 (Typora 0.9.86) on hiDPI...

Thanks for the quick response 👍 1. I removed the `--smoothLength` option as suggested and the warning goes away, however the error (same Traceback) still occurs. In Issue #550, @fidelram...

The ` AS:` string in the header was the problem. After figuring out that the chrom lengths were all zeros (via `writeBedGraph.getGenomeChunkLength`), I removed the ` AS:` string (and associated...

Hi - not the author, but you should look at the Jupyter notebook below, which has that exact plot and the context/code with which to generate it: https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/SCENIC%20Protocol%20-%20Case%20study%20-%20Cancer%20data%20sets.ipynb Note -...

Not the maintainer, but it's not clear what you are asking. Perhaps you can provide a more detailed description of what you are trying to do and provide code/commands.

Per regulon, the gene lists is formatted as a tuple within the `TargetGenes` column. If you want a simple comma-separate list of targets, per regulon, you'll need to parse that...

No problem. Indeed, some TFs have more than 1 motif, and some TFs can be hundreds+ target genes. That regulons object/file is the input to AUCell (see `pyscenic.transform.df2regulons`), so you...

Great! But so you know, I'm just another pySCENIC user like yourself. I roam these issues to learn more, and if I see stuff I can help with then it's...

no need to normalize - see https://github.com/aertslab/pySCENIC/issues/128#issuecomment-581324499

Probably incompatibility between `dask` and `distributed` packages. To avoid these issues, it's best to run pySCENIC from Docker image.