Re-running old SCENIC+ pipeline in the new version without snakemake

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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Re-running old SCENIC+ pipeline in the new version without snakemake #457

Closed skoturan closed 2 months ago

skoturan commented 2 months ago

Hi,

I'm struggling to reproduce my results done by the old SCENIC+ as my environment seems to have stopped working. Is there a way to look at the old files in the new version of SCENIC+?

Alternatively, do you have a detailed tutorial for using the new SCENIC+ to re-run all the steps in the pipeline from scATAC preprocessing with cisTopic, cisTarget, etc.? Hope you can help Thanks

SeppeDeWinter commented 2 months ago

Hi @skoturan

The tutorial can be found here: https://scenicplus.readthedocs.io/en/latest/tutorials.html

All the best,

Seppe

skoturan commented 2 months ago

Thank you for the new tutorial- I will try this!