Questions about AUCell's results

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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Questions about AUCell's results #490

Open qijt123 opened 1 year ago

qijt123 commented 1 year ago

Thank you for developing such a useful tool.

I would like to ask how pySCENIC can obtain the binary result of AUCell, that is, whether regulons is active information?

Looking forward to your reply!

SeppeDeWinter commented 1 year ago

Hi @qijt123

This binary result is obtained by thresholding the AUC distribution over cells.

To do this it is first tested wether this distribution is uni- or bi-modal (see example image below. The first one is unimodal, the second one is bimodal).

In case it's unimodal the threshold is set at the 95th percentile. In case it's bimodal the threshold is set to the threshold that best separates the two distributions.

I hope this helps

Best.

Seppe