Sayyam Shah
Sayyam Shah
Hello @ghuls, May you please respond to this? I have run pyscenic multiple times and increased the resources, yet I'm still experiencing the issue. The dataset consists of 270,000 cells....
Hello @SeppeDeWinter, I'm still able to run pyscenic on smaller datasets so I'm not exactly sure why I'm not experiencing the same issue for them. I ran it for 17...
Thank you so much! I emailed the manager of the HPC cluster and updated the GCC version.
Hello, I am also experiencing the same issue with 70k cells but this time with 300 GB and 20 cores. It has been stuck on the inferring regulatory network step...
I agree. The algorithm is not memory efficient. I have solved the issue with an alternative. I created meta cells using the tool below and inputted my own feature genes...
I would recommend aucell by scoring the top 100 genes from the signatures, however, an alternate method would be interesting.
Hello Haynes, Thank you for getting back to me so fast. I ran souporcell on both experiments while expecting k=6 donors. Initially, we didn't know how many donors made up...
Thank you for the amazing tool! I'm excited to implement seacells in my workflow; however, I'm experiencing the same problem with 30k cells on the HPC cluster with 184 GB.
That makes sense, thank you! I let it run for an hour before killing it since it did not complete a single iteration. I did not expect it to take...
That's amazing! I look forward to the GPU version.