pySCENIC aucell matrix is all 0s

Question

[Tripfantasy]

Hello,

Would anyone have an idea for how I am consistently getting an aucell matrix of all 0? I have run all other processes successfully. (grn, ctx) And my regulon data looks fine. There seems to only be a problem when producing the final aucell matrix.

[abby]

did you ever find a solution to this problem? I am having the same problem when running the test dataset from the tutorial (so the problem isn't my data!).

[Rachel]

having the same issue ...

[ziyanlin2352]

I am having the same issue.. any solutions? Many thanks in advance!

Answer 1

[Tripfantasy]

Sorry to those of you having the same issue. I haven't been on here in quite some time! I've documented my fix on pySCENIC's github page below:

https://github.com/aertslab/pySCENIC/issues/509

Best of luck!