Welcome to SCENIC+’s documentation!

SCENIC+ is a python package to build enhancer driven gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

SCENIC+ makes use of several python packages:

  • pycisTopic for enhancer candidate identification and topic modeling (read the docs page).

  • pycistarget for motif enrichment analysis in enhancer candidates (read the docs page).

  • create_cisTarget_databases for creating of custom cistarget databases (github page)


SCENIC+ is still under development. It is currently a beta version. Functions in this package may change in a future release.

SCENIC+ Flow chart

SCENIC+ flow chart