An R tool for prediction of gene regulatory networks from RNA-seq data. The GENIE3 algorithm uses the random forest or Extra-Trees approach.
Systems biology; Molecular interactions, pathways and networks; Gene expression; RNA-seq
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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