Scenic on HPC - Githubissues

aertslab / SCENIC

SCENIC is an R package to infer 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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Scenic on HPC #445

Open Sogand65 opened 4 months ago

Sogand65 commented 4 months ago

Hi,

I am using SCENIC on HPC and I have >57,000 cells, I checked and there are two versions available on the cluster for R: scenic-arrow/1.1 scenic/1.1 I am not sure which one to use, can anyone tell the differences? And can somebody please tell me what is the limit of cell numbers that can. be handled by SCENIC

thanks, Sogand

ghuls commented 2 months ago

Try to use pySCENIC instead of SCENIC (deprecated).

Container versions are available: https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images