Tutorials

SCENIC (R)

• Introduction and setup
• 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