User: scooter
scooter • 80
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Posts by scooter
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... An alternative to what Devon mentioned is to use the Cytoscape App Manager and install stringApp from there. Just go to Apps->App Manager and you can find the stringApp and install it. Alternatively, since you've already downloaded it, you can do an "install from file" from within the App Manag ...
written 9 days ago by
scooter • 80
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... In general, the cluster numbers are roughly ordered from largest cluster to smallest cluster, but each algorithm might treat these somewhat differently. Not sure why GLay isn't just ordering the clusters like other algorithms (e.g. MCL) do.
...
written 16 days ago by
scooter • 80
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... I think you need to add the CluePedia app to do that.
-- scooter
...
written 8 weeks ago by
scooter • 80
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... Greetings,
Sure here you go:
1. add the stringApp to Cytoscape 3.7.0
2. in the Network panel search bar, select STRING Protein Query
3. paste your genes of interest into the text box. Note that you should probably filter your gene list to those that show significant fold change and p-Value
...
written 8 weeks ago by
scooter • 80
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... 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 10 weeks ago by
scooter • 80
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... 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 4 months ago by
scooter • 80
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... 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 5 months ago by
scooter • 80
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... 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 10 months ago by
scooter • 80
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... You can use the enhancedGraphics app for this, which does work with 3.x
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written 10 months ago by
scooter • 80
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... 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 12 months ago by
scooter • 80
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Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: Nteworks in Cytoscape, time-series gene-expression
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