Need Good Cytoscape Tutorial
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10.5 years ago

Hello,

I am new to network analysis. I willing to use cytoscape for my work. Although cytoscape has tutorial, is there any advanced level tutorial to learn (with worked out example)?

cytoscape • 5.6k views
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10.5 years ago
jackuser1979 ▴ 890

Cytoscape has excellent manual with examples http://home.cc.umanitoba.ca/~psgendb/birchhomedir/BIRCHDEV/doc/cytoscape/manual.pdf

For further reading:

  1. Kohl et al. (2011) Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 696:291-303.(pmid: 21063955)
  2. Shannon et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-504. (pmid: 14597658)
  3. Cline et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-82. (pmid: 17947979)
  4. Killcoyne et al. (2009) Cytoscape: a community-based framework for network modeling. Methods Mol Biol 563:219-39. (pmid: 19597788)
  5. Smoot et al. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431-2. (pmid: 21149340)
  6. Merico et al. (2011) Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods Mol Biol 781:257-77.(pmid: 21877285)
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I particularly found this paper very helpful:"Cline et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-82. (pmid: 17947979)"

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10.5 years ago

The best thing is to ask to the Cytoscape Mailing list. Moreover, there are many workshop about Cytoscape; you may find materials about them in slideshare and in google.

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