graphite

Oct 9, 2019 r
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Graphite framework is divided in two main steps

  • The conversion procedure that create the networks
  • The R package that allows the use and the analyses of the network within the BioC platform,
  • The Web tool GraphiteWeb that allows the use and the analyses of the network directly on the web.

The BioC graphite package is constantly updated and available at the BioC site.

GraphiteWeb is freely available here and is based on the graphite BioC package and on our pathway analysis pipelines.

Sales G, Calura E, Cavalieri D, Romualdi C (2012). “graphite - a Bioconductor package to convert pathway topology to gene network.” BMC Bioinformatics. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-20.

Sales G, Calura E, Romualdi C (2018). “metaGraphite - a new layer of pathway annotation to get metabolite networks.” Bioinformatics. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty719/5090451.

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