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SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
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README.md

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:

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:

2018/06/20:

2018/06/01:

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

2018/05/01:

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.
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