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pySCENIC

pySCENIC

A Python pipeline for inference of gene regulatory networks and identification of cell states in RNA-seq data sets. The pySCENIC workflow is a Python implementation of the original SCENIC R package and much faster (see links).

Topic

RNA-seq; Molecular interactions, pathways and networks; Gene expression; Transcription factors and regulatory sites

Details

  • Operation: Gene regulatory network analysis; Gene expression analysis; RNA-Seq analysis
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Other
  • Cost: Free for non-commercial usage
  • Version name: 0.9.19
  • Maturity: Stable
  • Credit: The Research Foundation - Flanders (FWO), Special Research Fund (BOF) KU Leuven, Foundation Against Cancer, Belgium, ERC Consolidator Grant, PDM Postdoctoral Fellowship - the KU Leuven, postdoctoral research fellowships from Kom op Tegen Kanker, F.R.S.-FNRS Belgium, the agency for Innovation by Science and Technology (IWT), Symbiosys and IMEC HI^2 Data Science.
  • Contact: Stein Aerts stein.aerts _at_ kuleuven.vib.be
  • Collection: SCENIC

Publications

Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo González-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S. "A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain." Cell. 2018 Aug 9;174(4):982-998.e20. https://doi.org/10.1016/j.cell.2018.05.057
PMID: 29909982
PMCID: PMC6086935


Aibar S, Gonzalez-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S "SCENIC: single-cell regulatory network inference and clustering." Nat Methods. 2017 Nov;14(11):1083-1086. https://doi.org/10.1038/nmeth.4463
PMID: 28991892
PMCID: PMC5937676


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