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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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How to run SCENIC+ with Signac processed data #499

Open zhli12 opened 2 weeks ago

zhli12 commented 2 weeks ago

Hello,

Is there a recommended workflow to run SCENIC+ on data processed by Signac? I saw there was a tutorial: https://pycistopic.readthedocs.io/en/latest/Toy_melanoma-RTD.html, which I found on the FAQ page https://scenicplus.readthedocs.io/en/latest/faqs.html#i-have-an-analysis-with-another-tool-e-g-signac-archr-can-i-still-use-scenic, but the tutorial is no longer accessible (404 not found). Does anyone know what is the correct procedures to convert a Signac object in R to a CisTarget in Python, or whether there is an updated tutorial on this? Thanks!

mluciarr commented 5 days ago

I am wondering the same!! I would appreciate it if you could answer this question. Because reprocessing all the data again in python will be very time-consuming. thanks in advanced

SeppeDeWinter commented 4 days ago

Hi @zhli12 and @mluciarr

You can still find this tutorial here: https://github.com/aertslab/pycisTopic/blob/old/notebooks/Toy_melanoma-RTD.ipynb

All the best,

Seppe

Sebdumas commented 1 day ago

Hi @SeppeDeWinter ,

Following up on this topic ;) : considering I already have performed DAR analysis in Signac, do you suggest to rerun these analyses with pycisTopic ? or can I simply use my previous DAR analysis output from Signac + topics obtained from pycisTopic to run Scenicplus ?

My understanding of the tutorial is that DAR analysis in pycisTopic is somehow influenced by the topics, right? But I am not sure if it is actually beneficial in the scenicplus pipeline.

Thank you for your input,

Kind regards, Sébastien