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