Seppe De Winter

Hi @Sayyam-Shah To get more info on the warning message please see this answer on stack overflow: https://stackoverflow.com/a/48664628/16278776 That being said, this warning message is not necessarily an issue, but...

Hi @nasjr08 Great remark!! You are right, we have to update the list of TFs. You are also right that you can just add them to the file. As to...

Hi First of all would you mind sharing which 2 TFs you are interested in, that way I can also check wether they are missing from our databases. The motif-to-TF...

Hi ` Ah I see, That's massively helpful. I have actually checked the TF motifs in the motifs-v9-nr.hgnc-m0.001-o0.0.tbl and they all appear to be there. I am looking at PRRX1...

Please see following issues where your question is already adressed: https://github.com/aertslab/pySCENIC/issues/376 https://github.com/aertslab/pySCENIC/issues/356 https://github.com/aertslab/pySCENIC/issues/320

Hi @Erfan1369 The error `numpy.core._exceptions.MemoryError: Unable to allocate 3.11 GiB for an array with shape (17627, 23657) and data type float64` suggests you don't have enough memory available on your...

Hi I changed the label of this issue because it is likely that the error you encountered is not caused by a bug in the pyscenic code. How many target...

Three genes is probably too low to calculate the enrichment values using AUCell. You can consider excluding these regulons to be able to draw your heatmap. Best, Seppe

Hi Jens We indeed mostly use these values relatively (e.g. by taking the top n target genes per TF based on the importance score), their absolute value alone is not...

Hi @chentongouc Which cistarget databases are you using? (i.e. what is stored in the `$f_db_names` variable?)