User: scooter

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scooter60
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Posts by scooter

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Importing networks from Cytoscape public database is very very slowly!
... What public database service are you using? I've been using STRING (through stringApp) a lot lately and it's been working fine for me. ...
written 3 days ago by scooter60
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Answer: A: Nteworks in Cytoscape, time-series gene-expression
... Hi Malgosia, Importing the data shouldn't be a problem. Each of your conditions would be a separate column, and you can color the nodes by the expression value in that column. Pathway enrichment would be a little trickier, but fundamentally just the same basic steps repeated over and over: 1. ...
written 11 weeks ago by scooter60
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Answer: A: Small pathways but big network files
... What version of Cytoscape are you using? There was certainly a problem with previous versions not deleting rows/nodes in the root network, but I think it should be *much* better now. -- scooter ...
written 12 weeks ago by scooter60
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Answer: A: Cytoscape : how to color same nodes with several colors ?
... Sorry -- this should have been an answer, not a comment. You can use the enhancedGraphics app for this, which works fine in 3.x. The app store points to documentation on how to set things up. ...
written 8 months ago by scooter60
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Comment: C: Cytoscape : how to color same nodes with several colors ?
... You can use the enhancedGraphics app for this, which does work with 3.x ...
written 8 months ago by scooter60
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Answer: A: How to color nodes in Cytoscape according to expression of genes? How should the
... The two columns are the start and end and in the example you provided, they were obtained by a yeast-two-hybrid experiment. Sounds like you don't have any PPI data -- just your expression values. There are two approaches I can suggest. 1. Just import your data with "Source Node" and two "Source ...
written 10 months ago by scooter60
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Answer: A: how can we show in Cytoscape the types of interactions among gene-TF
... Hi Fereshteh, You could read that file in as a network, then use the Cytoscape Style panel (look at the Edge tab) and change the arrow type (or edge color, if you want) to reflect whether it's activation or repression. -- scooter ...
written 15 months ago by scooter60
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Answer: A: How to properly export cytoscape GO network as pdf without cut-offs
... Greetings, Well, it's hard to know that the problem might be without seeing your network. In general, however, the PDF export from Cytoscape should show exactly what's on the screen. You may need to zoom out a little if your nodes are really close to the edge, but other than that, there should ...
written 18 months ago by scooter60

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Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Nteworks in Cytoscape, time-series gene-expression

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