SCENIC specifications


Unique identifier OMICS_18781
Alternative name Single Cell rEgulatory Network Inference and Clustering
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Stein Aerts

Publication for Single Cell rEgulatory Network Inference and Clustering

SCENIC citation


Using single‐cell genomics to understand developmental processes and cell fate decisions

Mol Syst Biol
PMCID: 5900446
PMID: 29661792
DOI: 10.15252/msb.20178046

[…] small differences can be readily confounded by technical artefacts (e.g. batch effects), and inference of gene regulatory networks from scRNA‐seq data has been challenging to date. For instance, the SCENIC package utilises cis‐regulatory information to reinforce transcriptional gene network learning (Aibar et al, ).One possible solution to this problem is the combination of single‐cell RNA‐seq wi […]

SCENIC institution(s)
VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium; KU Leuven, Department of Human Genetics, Leuven, Belgium; KU Leuven ESAT/STADIUS, VDA-lab. Leuven, Belgium; IMEC Smart Applications and Innovation Services. Leuven, Belgium; KU Leuven, Department of Imaging and Pathology, Translational Cell and Tissue Research, Leuven, Belgium; University of Liège, Department of Electrical Engineering and Computer Science, Liège, Belgium; VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium; KU Leuven, Department of Oncology, Leuven, Belgium
SCENIC funding source(s)
Supported by The Research Foundation - Flanders (FWO, grants G.0640.13 and G.0791.14), Special Research Fund (BOF) KU Leuven (grants PF/10/016 and OT/13/103), Foundation Against Cancer (2012-F2) and ERC Consolidator Grant (724226_cisCONTROL); by a PDM Postdoctoral Fellowship from the KU Leuven; by postdoctoral research fellowships from Kom op Tegen Kanker and by a PhD Fellowships from the agency for Innovation by Science and Technology.

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