User: scooter

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scooter80
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Posts by scooter

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Automatic Coloring for Each Node According to Names in Cytoscape
... Hi, Definitely, you can set up a discrete mapper and then you can right-click and select "Mapping Value Generators" and choose one of the generators. Note that 18 different colors is probably too many for a user to distinguish, but it might be useful for exploration. ...
written 10 days ago by scooter80
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Comment: C: Nodes and attributes in Cytoscape NA
... I'm not sure I can answer the question of "validity" with just the description you've given us. Some additional information might help: 1. It sounds like you are creating a bi-partide network, with food classes as one type of node and gene-targets as another. Is that right? 2. I'm not clear how ...
written 10 weeks ago by scooter80
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Answer: A: Cytoscape Nodes/Interactions Export
... Hi Michael, Do you mean export a set of currently selected nodes and their interactions? As you stated, SIF will give you a table of all nodes and their partners. If you want specific nodes and their partners, what I would do is to select the nodes you want to include, select all of the first n ...
written 10 weeks ago by scooter80
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Answer: A: Difficulty in opening downloaded stringApp.jar file
... 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 5 months ago by scooter80
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Answer: A: What does cluster number in ClusterMaker represent?
... 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 5 months ago by scooter80
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Answer: A: how to add gene name in cluego?
... I think you need to add the CluePedia app to do that. -- scooter ...
written 7 months ago by scooter80
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Answer: A: Creating interaction network using cytoscape
... 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 7 months ago by scooter80
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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 7 months ago by scooter80
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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 10 months ago by scooter80
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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 10 months ago by scooter80

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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Nteworks in Cytoscape, time-series gene-expression

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