[BUG]Expression matrix should be provided in the loom file format/The loom doesn't contain regulon information

aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

http://scenic.aertslab.org

GNU General Public License v3.0

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[BUG]Expression matrix should be provided in the loom file format/The loom doesn't contain regulon information #527

Open HaixJiang opened 6 months ago

HaixJiang commented 6 months ago

Describe the bug

pySCENIC
pyscenic aucell 
pyscenic.cli.pyscenic - ERROR - Expression matrix should be provided in the loom file format.
R-SCENIC
regulons_incidMat <- get_regulons(sce_SCENIC, column.attr.name="Regulons")
The attribute 'Regulons' is not available in this loom file. The loom doesn't contain regulon information

I encountered the two bugs mentioned above, and I was able to resolve them by downgrading the software version. I'll provide the version numbers of the two software packages below, which may offer some solutions for future users and also provide the authors with some inspiration for updates.

-pySCENIC==0.12.1
-loompy==3.0.1
-pandas==1.5.3

FourAlarmFire commented 5 months ago

I just encountered too with the same code and same error. do you resolve this problem? thanks

HenryJinZH commented 4 months ago

I just encountered with the same code and same error too!!! do you resolve this problem? thanks a lot

FourAlarmFire commented 4 months ago

NO，I did not. I still could not resolve it.

---- Replied Message ---- | From | @.> | | Date | 03/30/2024 00:02 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [aertslab/pySCENIC] [BUG]Expression matrix should be provided in the loom file format/The loom doesn't contain regulon information (Issue #527) |

I just encountered with the same code and same error too!!! do you resolve this problem? thanks a lot

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chenhy-lab commented 4 months ago

too

rhlgyb commented 3 months ago

same here

wangtanzhang612 commented 1 month ago

I just encountered with the same code and same error too!!! do you resolve this problem? thanks

HaixJiang commented 1 month ago

I was able to resolve them by downgrading the software @wangtanzhang612

RickyMaGZ commented 1 month ago

which version did you downgrade pyscenic to? I've encountered the same issue. thanks @HaixJiang