User: scooter

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scooter110
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Posts by scooter

<prev • 20 results • page 1 of 2 • next >
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Answer: A: How to show selected node lables only in cytoscape?
... There are two approaches to do what you want: 1. Create a new column and just copy over the labels you want to show and leave the others blank. Then you can use that column as a passthrough to your node label. 2. I would just select the nodes you want to show the labels for, then invert the sele ...
written 28 days ago by scooter110
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Answer: A: ClueGO - Cytoscape - GO terms
... From the Supplementary material in their [paper][1]: "ClueGO allows also KEGG updates via SOAP API. ClueGO KEGG based files will have in the name the date of the download. The KEGG update rate: http://www.genome.jp/en/info dbget.html. Since Biocarta is not frequently changing and only supports huma ...
written 6 weeks ago by scooter110
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Answer: A: Is "Attribute Circle Layout" of a protein-protein network standard and acceptabl
... You may also want to take a look at the recently published paper: ["Ten simple rules to create biological network figures for communication"][1] to see if that gives you some ideas on how to proceed. -- scooter [1]: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007244 ...
written 6 weeks ago by scooter110
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Comment: A: Cytoscape, cannot delete column
... Greetings, You don't what version of Cytoscape you are using, which might be helpful. In any case, if you can send me your network, I can quickly tell you what the problem is. The Cytoscape API does allow you to create immutable columns, but I'm not familiar enough with DyNet to know if they do ...
written 6 weeks ago by scooter110
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Answer: A: Adding more nodes to a PPI network?
... Well, the honest, but somewhat unhelpful, answer is "it depends". What is your p-Value based on? Are you doing some kind of GO enrichment? Where did your initial gene list come from? It's certainly possible that there are key proteins in pathways that aren't captured by typical transcriptomics o ...
written 3 months ago by scooter110
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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 4 months ago by scooter110
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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 6 months ago by scooter110
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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 6 months ago by scooter110
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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 9 months ago by scooter110
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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 9 months ago by scooter110

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Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Nteworks in Cytoscape, time-series gene-expression

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