search

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
448 stars 183 forks source link

[BUG] #584

Open aterceros opened 1 month ago

aterceros commented 1 month ago

Hi, First time running the pySCENIC pipeline, and would like to export the loom file but having an issue when running export2loom(), Erro message is: AttributeError: module 'numpy' has no attribute 'msort'. Do you recommend downgrading numpy? I currently have numpy 2.0.2. Thank you

ghuls commented 1 month ago

numpy 2.0 deprecated a lot of the old numpy API, so it is likely to give a lot of issues. Downgrade to a 1.x version. If you use the latest git version of pySCENIC, the latest numpy release of the 1.26.0 should normally work. Otherwise you need numpy <1.24.0.

aterceros commented 1 month ago

thank you so much! downgrading fixed it!