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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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Which Cytoscape version to use with current version of spade R library? #110

Closed SamGG closed 9 years ago

SamGG commented 9 years ago

Hi,

I tried 2.8.3 on Windows 7 and Linux Mint. Although computation are done within R, no way to use Cytoscape plugin to view and analyze the result. Any clue? Should I switch to Cytoscape 3.x?

Best

zbjornson commented 9 years ago

Hello, We've essentially stopped supporting Cytoscape. Soon we're releasing a Gephi plugin with basic functionality for viewing SPADE trees. Meanwhile, you can import GML files in Cytoscape and explore a bit that way, or try the fully supported version in Cytobank (www.fluidigm.cytobank.org). Best, Zach

SamGG commented 9 years ago

Thanks for your answer Zach. I have already imported GML in Cytoscape and play around. That's good, but the plugin allowed density plot which was as very nice feature. I guess you mean that such a feature will not be ported to Gephi. I played also with Cytobank, but not all users would pay for it. Apart from the visualisation/gating part, are the R codes stable and roughly the same as Cytobank ? Best.

zbjornson commented 9 years ago

The plot will be ported, yes. The T test will likely not be ported.

The R code is stable and is the same used in Cytobank.

SamGG commented 9 years ago

Yeah, the plot is the major feature needed. Thanks. Let us know when a alpha/beta version is available for testing. Best.