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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
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Similare Transcription factor in TF resources #511

Open Erfan1369 opened 10 months ago

Erfan1369 commented 10 months ago

**Hello Scenic developers,

I wanted to express my gratitude for creating such an amazing tool. I've used SCENIC to analyze single-cell data that we're interested in incorporating into our Nextflow pipeline.

I have a question regarding the regulon.csv file, which contains all possible regulons. The tool considers Sf1 and Nr5a2 as different regulons (we have Sf1 (+) and Nr5a1(+) in the output); however, they are the same regulon with different annotations. Is Nr5a1 considered a distinct regulon in the transcription factor (TF) sources compared to Sf1? Or is there any other specific reason (such as motif resources, etc.) for having both of them in the TF resource? I would appreciate any clarification on this matter.

Thank you.**

ghuls commented 7 months ago

Each regulon predicts which genes a certain TF regulates. So it is possible that 2 distinct TFs have the the same target genes predicted.