JZ

could be that the number of genes you had in you anndata object is too few.

Running into this problem, to me clearly, the author did not translate the formula correctly into this package. As far as I can tell, the calculation in this package is...

had the same issue, upon checking, found that the utli.py file was written wrong. to fix this, please 1.change "import scipy as sp" to "import numpy as np" 2. replace...

I did a research on this issue, the problem stems from the [checkAnnots] and [dbLoadingAttempt]function (https://rdrr.io/github/aertslab/SCENIC/man/ScenicOptions-class.html). checkAnnots has designated rnktype = "features", therefore, even if you have changed the dbIndexCol=''motifs",...

> It's been a while since I was trying this, my recollection was that I could run through all the steps without any issues after making those changes, but the...

For anyone who really wants to use the new database, it's probably a better investment of your time to run the latest pySCENIC, instead of trying to hack this in...

I'm not sure if you should use their most recent database, it appears to me that the number of TFs in the new database is the same as the old...

I think the idea is good, but I think the posted code is wrong. also, you need to be careful when use all cores to do the calculation, ram will...

I think the original color gradient implementation is probably a better one, I had a hard time to understand what the blend.threshold actually does, as it turns out to be...