User: scooter

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scooter420
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Posts by scooter

<prev • 74 results • page 1 of 8 • next >
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Answer: A: Interaction Network Cytoscape
... I think you can do step 2 with a little preprocessing also, but depending on the size of your network, it would probably require some scripting. In any case, I can't think of an App that does exactly what you want, unfortunately, but here is a way to think about it. You want to add an edge between ...
written 5 days ago by scooter420
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Answer: A: Cytoscape crashes when importing a network with Cy3D as renderer
... Greetings, Well, the first problem is that Cytoscape 3.8 requires Java 11. Can you try upgrading to OpenJDK 11 and try again? -- scooter ...
written 12 days ago by scooter420
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Answer: A: Cytoscape Directed Network Layout
... Greetings! The easiest way to do that is to add a column (say, call it Type) that states what the node type is. Then you can easily set up a discrete map to color according to type. You would probably want to do that in your input file before importing it into Cytoscape. -- scooter ...
written 12 days ago by scooter420
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Answer: A: What is the most efficient way of discovering bait-prey interaction networks and
... Greetings, What biological question are you attempting to answer? That is, tell us what the figure caption is meant to show. You've done a pull down experiment with a single bait, so your network has 400 edges, from the bait to each of the 400 proteins you've pulled down. You could use the string ...
written 5 weeks ago by scooter420
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Answer: A: Protein atlas networks in cytoscape
... Hi Lir, Unfortunately, I don't know of an easy way to get from the network of cells and proteins to a network just of cells with counts on the edges. My knee-jerk would be to export the data as a table and then process the table using python or some external program to give a new network with a ...
written 6 weeks ago by scooter420
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Answer: A: Create a new network that uses miRNA-gene and gene-gene interactions to link a l
... Greetings, and welcome to Cytoscape. I think there are a couple of plugins that might be useful. What I would suggest is to use your list of genes and then probe one of the databases to explore how those genes might be related. For example, you could use the stringApp, add your list of genes, but ...
written 6 weeks ago by scooter420
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Answer: A: Which tool for clustering (sub-networking) of protein-protein interaction networ
... Answered on the Cytoscape helpdesk: https://groups.google.com/g/cytoscape-helpdesk/c/qFE4nf4o_xU ...
written 6 weeks ago by scooter420
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Answer: A: Unable to download new organisms in ClueGO (cytoscape)
... Sorry to hear about your problem. The best bet would be to contact the authors of ClueGO directly -- in general they are extremely responsive. Look for the "E-Mail" link on the app store page for ClueGO. -- scooter ...
written 6 weeks ago by scooter420
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Answer: A: Add pentagon node shape to cytoscape
... At this point, we don't support a pentagon shape. You could perhaps fake it by using an image of a pentagon and mapping that onto the node. We have hexagons and octagons, but no pentagons, unfortunately. -- scooter ...
written 7 weeks ago by scooter420
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Answer: A: Problem loading data from metadata file on Cytoscape
... Typically, this happens when there is a mismatch between the "Key Column for Networks", which you have set to "shared name" and the column in your spreadsheet to use to match it. I don't see what column you've selected to match the shared name column, but the values in those columns have to match i ...
written 7 weeks ago by scooter420

Latest awards to scooter

Scholar 6 weeks ago, created an answer that has been accepted. For A: How to show selected node lables only in cytoscape?
Scholar 3 months ago, created an answer that has been accepted. For A: How to show selected node lables only in cytoscape?
Scholar 7 months ago, created an answer that has been accepted. For A: How to show selected node lables only in cytoscape?
Scholar 9 months ago, created an answer that has been accepted. For A: How to show selected node lables only in cytoscape?
Scholar 10 months ago, created an answer that has been accepted. For A: How to show selected node lables only in cytoscape?
Scholar 10 months ago, created an answer that has been accepted. For A: How to show selected node lables only in cytoscape?
Scholar 15 months ago, created an answer that has been accepted. For A: How to show selected node lables only in cytoscape?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Nteworks in Cytoscape, time-series gene-expression

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