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SCENIC is deprecated, use pySCENIC instead.

SCENIC

SCENIC (Single-Cell rEgulatory Network Inference and Clustering) is a computational method to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

The description of the method and some usage examples are available in Nature Methods (2017).

There are currently implementations of SCENIC in R (this repository), in Python (pySCENIC), as well as wrappers to automate analyses with Nextflow (VSN-pipelines).

The output from any of the implementations can be explored either in R, Python or SCope (a web interface).

Tutorials

If you have access to Nextflow and a container system (e.g. Docker or Singularity), we recommend to run SCENIC through the VSN-pipeline.

This option is specially useful for running SCENIC on large datasets, or in batch on multiple samples.

If you prefer to use R for the whole analysis, these are the main tutorials:

The tutorials in R include a more detailed explanation of the workflow and source code.

Python/Jupyter notebooks with examples running SCENIC in different settings are available in the SCENIC protocol repository.

Frequently asked questions: FAQ


News

2021/03/26:

2020/06/26:

2019/01/24:

2018/06/20:

2018/06/01:

2018/05/01:

2018/03/30: New releases