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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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[results] Bulk RNA-seq + (pseudobulked?) scRNA-seq? #359

Closed mcsimenc closed 2 years ago

mcsimenc commented 2 years ago

Hi, I have a question about using bulk RNA-seq and scRNA-seq with SCENIC for a single analysis. Would it be advisable to run SCENIC using a concatenated bulk RNA-seq matrix and a pseudobulked single cell matrix (or full scRNA-seq matrix?), or better to run SCENIC separately on both data sets and combine the results?

SeppeDeWinter commented 2 years ago

Hi @mcsimenc,

This is something we have never tried before. You could try both approaches.

For concatenating bulk RNA-seq and scRNA-seq, I'm afraid this will cause a batch effect due to the two data modalities (e.g. differences in sensitivity of both techniques). This may affect the target genes that are being picked up. I would be careful with this and it would probably need some sort of normalisation to remove this effect.

Running SCENIC separately on both datasets and combining afterwards also is not trivial.

I'm afraid I don't have an easy solution here for you. This is not really what SCENIC was designed for, so it will need some trial and error from your side. I'm not saying that it is impossible to do of course.

Do report back though, I'm curious to see if and how you get it to work.

Good luck.

Seppe

mcsimenc commented 2 years ago

I will let you know how this turns out if I do it. Thanks!

SeppeDeWinter commented 2 years ago

Good luck! Very curious!