Running SCENIC

Jupyter notebooks to run SCENIC from VSN

Explore its output (with SCope and R) (edited)

pySCENIC (Python)

pySCENIC tutorials

SCENIC with VSN-Pipelines (Nextflow DSL2)

Case study with 10x Genomics public data

SCENICprotocol (Nextflow DSL1)

PBMC 10k dataset (10x Genomics)

Full SCENIC analysis, plus filtering, clustering, visualization, and SCope-ready loom file creation:

Jupyter notebook | HTML render

Extended analysis post-SCENIC:

Jupyter notebook | HTML render

To run the same dataset through the VSN Pipelines DSL2 workflow, see this tutorial .

Cancer data sets

Jupyter notebook | HTML render

Mouse brain data set

Jupyter notebook | HTML render

SCENIC+ (Python)

From count matrix and fragments file to enhancer driven gene regulatory network (eGRN)

Running SCENIC+ step by step

SCENIC+ analysis on non-multiome data: separate scATAC-seq and scRNA-seq on different cells of the same sample

Transcription factor perturbation simulation

Unbranched GRN velocity

Branched GRN velocity