SCENIC

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

For more details and installation instructions see the tutorials:

• Introduction and setup
• running SCENIC

The output from the examples is available at: http://scenic.aertslab.org/examples/

Frequently asked questions: FAQ

Use pySCENIC for a lightning-fast python implementation of SCENIC.

News

2019/01/24:

• Tutorial for importing pySCENIC results in SCENIC by using loom files.

2018/06/20:

• Added function export2scope() (see http://scope.aertslab.org/).
• Version bump to 1.0.

2018/06/01:

• Updated SCENIC pipeline to support the new version of RcisTarget and AUCell.

2018/05/01:

• RcisTarget is now available in Bioconductor.
• The new databases can be downloaded from https://resources.aertslab.org/cistarget/.

2018/03/30: New releases

• pySCENIC: lightning-fast python implementation of the SCENIC pipeline.
• Arboreto package including GRNBoost2 and scalable GENIE3:
  • Easy to install Python library that supports distributed computing.
  • It allows fast co-expression module inference (Step1) on large datasets, compatible with both, the R and python implementations of SCENIC.
• Drosophila databases for RcisTarget.