Revision 3ab64a149ec4ef26ea56faba5d0670c5c1bf759d authored by alexandregrimaldi on 14 April 2021, 11:25:11 UTC, committed by GitHub on 14 April 2021, 11:25:11 UTC
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README.md
# DriverRegulators
Identify transcription factors underlying cell state transitions in scRNAseq datasets
This repository contains the source code and information regarding the DriverRegulators pipeline (Grimaldi et al. 2021).
## Workflow
This juyter notebook code combines the output of 2 python libraries, pyscenic and scvelo, into a network of transcription factors and associated target genes.
The general workflow is:
1-Running scvelo and saving the top driver genes by cluster as a table
2-Extracting the AUC matrix and the regulons from the f_final.loom file of pyscenic output
3-Generate tables of Nodes and Edges based on interactions found in a given cluster
4-Using a program such as Gephi to visualize the network
Computing file changes ...
