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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Running Scenic+ without Snakemake #510

Open gilgolan73 opened 3 days ago

gilgolan73 commented 3 days ago

Hello, I am encountering an issue with running Scenic+ using Snakemake (see issue #468), as instructed by the tutorial https://scenicplus.readthedocs.io/en/latest/human_cerebellum.html#Running-SCENIC+ . Is there a possibility to run the rest of Scenic+ pipeline without Snakemake ? (but in a regular python code, as instructed by the old tutorial https://scenicplus.readthedocs.io/en/stable/pbmc_multiome_tutorial.html, or by another tutorial?).

Thank you, Gil

SeppeDeWinter commented 3 days ago

Hi @gilgolan73

Yes, you can run the individual commands that are normally run within the Snakemake pipeline. See: https://github.com/aertslab/scenicplus/blob/main/src/scenicplus/snakemake/Snakefile for more info.

Best,

Seppe