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Arboreto

Arboreto

Arboreto is a tool to infer gene regulatory networks in RNA-seq data. The Arboreto framework uses GRNBoost2 and an improved GENIE3 version. GRNBoost2 uses a gradient boosting approach for gene network inference.

Topic

RNA-seq; Molecular genetics; Gene regulation; Transcriptomics

Details

  • Operation: Gene regulatory network analysis
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: BSD 3-Clause "New" or "Revised" License
  • Cost: Free
  • Version name: 0.1.5
  • Maturity: Emerging
  • Credit: IMEC Strategic Funding, IWTExaptation, FWO 06260, Special Research Fund (BOF) KU Leuven, ERC Consolidator Grant, Foundation Against Cancer.
  • Contact: thomas.moerman _at_ esat.kuleuven.be, stein.aerts _at_ kuleuven.vib.be
  • Collection: -

Publications

Moerman T, Aibar Santos S, Bravo Gonzalez-Blas C, Simm J, Moreau Y, Aerts J, Aerts S "GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks." Bioinformatics. 2019 Jun 1;35(12):2159-2161. https://doi.org/10.1093/bioinformatics/bty916
PMID: 30445495


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