Lucy Garner

Thank you - yes I have tried using `dask=1.0.0`, `distributed >=1.21.6, ERROR: pyscenic 0.10.1 has requirement dask==1.0.0, but you'll have dask 2.11.0 which is incompatible. > ERROR: pyscenic 0.10.1 has...

I am using Conda environments, so if you have a .yml file for a Conda environment where pyscenic is working, I could give that a try

Thank you @cflerin, I have tried using the `arboreto_with_multiprocessing.py` script. I am now getting the following error with both approaches (`pyscenic grn` or `arboreto_with_multiprocessing.py`) > 2020-06-04 20:37:40,351 - pyscenic.cli.pyscenic -...

Thank you - I will update to 0.10.2. This is my command for `arboreto_with_multiprocessing.py` - can you see anything wrong with this? `python arboreto_with_multiprocessing.py data/merged_all_analysed.loom resources/tfs_list/lambert2018.txt --output results/adjacencies.csv --num_workers 20`

Hi @Annika18, I couldn't find the script within the package either, so I just copied it from the GitHub page. It should then be possible to run the script from...

Hi @Annika18, This is likely because most people will be running pySCENIC on a high performance computing cluster. If you only have 4 cores available, then you should go with...

Thank you. I have an activation dataset so the RNA composition will be altered significantly in the different groups, so genes that don't change upon activation will likely be under-sampled....

What is the reason for the use of normalised data for pySCENIC in this publication from the Aerts lab? https://www.nature.com/articles/s41556-020-0547-3

Why do so many papers use --shift -100 --extsize 200 for MACS2 rather than -f BAMPE if this is not recommended for paired-end data?

Ok thank you. But you would still recommend the -f BAMPE option? After peak calling with -f BAMPE, I then take the 5' end of the forward and reverse reads...