compare between different conditions

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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compare between different conditions #570

Open Sirin24 opened 2 months ago

Sirin24 commented 2 months ago

Hello, i want to compare between 3 different conditions. do i run pyscenic on each disease and its control only ? or on a subset of the whole object. I noticed the highest RSS is the same TF for the celltype_disease and celltype_control when the file contained 1 condition and its control. Should they be separated?

If I separate then when it is time for the auc step do I need to have all 3 conditions present in the same object so that the activities be comparable?

anemartinezlarrinaga2898 commented 1 month ago

Hello Im facing the same question, I did not try to run it but I was wondering on which way would be the most appropriate?

Thaaaanks!