SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Perturbation effect issue, One sample has ~0 perturbation scores for all TFs #405
This is an issue with the output of perturbation analysis, but not a hard error.
I ran the exact same code on all three samples, however one the sample with the highest number of cells had an issue that the perturbation effect of all TFs is ~0, I not sure why this happens as the other steps worked fine in the SPLUS analysis of this sample
The perturbation HM is =0 for all clusters and TFs except one cluster ( Late-EMT-2 )
This sample also had the highest amount of significant / high quality regulons so it took much longer to run, well over 6 hours while the other samples took <2 hours, so I would've expected it to work better since it has more statistical power.
Any ideas ?
relevant software versions
velocyto v 0.17.17
scanpy v 1.9.6
pandas v 1.5.0
numpy v 1.24.4
scenicplus v 1.0.1.dev4+ge4bdd9f
Python version 3.8.18
This is an issue with the output of perturbation analysis, but not a hard error.
Any ideas ?
relevant software versions velocyto v 0.17.17 scanpy v 1.9.6 pandas v 1.5.0 numpy v 1.24.4 scenicplus v 1.0.1.dev4+ge4bdd9f Python version 3.8.18