User: xanderpico

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xanderpico150
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Posts by xanderpico

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Bipartite network analysis using cytoscape
... You might try the Centiscape app. I'm not sure if it handles bipartite graphs, but it is a popular alternative to the built-in Network Analyzer. http://apps.cytoscape.org/apps/centiscape ...
written 9 days ago by xanderpico150
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Answer: A: Cytoscape's plugin 'stringApp' error
... In Cytoscape, the stringApp installs into the network search bar at the top of the Control Panel. I think this is where you are pasting/typing your list of gene symbols, which is correct. Before clicking on search (the magnifying glass icon), however, you will want to click on settings (the three li ...
written 6 weeks ago by xanderpico150
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Answer: A: Cytoscape: select edges that are the interactions between two networks
... There's an app for that! We developed an app for managing sets of nodes or edges, called setsApp: http://apps.cytoscape.org/apps/setsapp After you install the app, follow these steps: 1. Drag select all edges in network B 2. Click on the "Sets" tab in the Control Panel 3. Click the + button near ...
written 8 weeks ago by xanderpico150
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Comment: C: Cytoscape 3.3.0 visualize network with up/down regulated color
... Great description. I'll just add that in the last step, when you're assigning colors to each category, you can alternatively right-click anywhere on that property, choose Mapping Value Generators, and then select a preset range of colors to automatically perform the assignment. This is helpful when ...
written 10 weeks ago by xanderpico150
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Answer: A: Multiple networks integrated into one figure in Cytoscape
... Sure. Cytoscape has a merge tool (see Tools>Merge>Networks). You could perform a UNION merge of the three networks (n1-3) to get a merged network (n4). Then using the search tool (upper right), you can paste in your lists (l1-3), one at a time to select the nodes per species. To track the nod ...
written 3 months ago by xanderpico150
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Answer: A: Ideas for more analysis
... There are indeed many directions you could go within Cytoscape. As mentioned before, much of this depends on what your biological question is, as well as what data you have. Key information is missing for me to give you a specific answer, e.g., how did you get the original network that you then clus ...
written 4 months ago by xanderpico150
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Answer: A: Visualising all KEGG metabolism in Cytoscape
... Looking at the output you have already generated, I think you will need to make "reaction nodes" in addition to nodes representing molecules. You'll then need to parse reactants (R) and products (P) per reaction (X) from your current file into a two-column format that looks like this: source ...
written 8 months ago by xanderpico150
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Answer: A: Cytoscape - "Ontology and Annotation" import window not opening
... It is a bug. Turns out that the service has been broken for a while. We have removed the menu item in the next version, due next month. And we have issued a feature request to replace this functionality with a new service. ...
written 9 months ago by xanderpico150
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Answer: A: expression to networking
... Perhaps a bit late, but given a single differential expression result, I typically go to a resource like GeneMANIA to generate a network based on more comprehensive co-expression analysis and then import that into Cytoscape. Then I overlay my diff exp data onto that network to assess the "functional ...
written 9 months ago by xanderpico150
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Informatics On Biologists: Author Affiliations
... As long as informatics on biologists counts as "bioinformatics", I hope this question can find an answer here... I am trying to build a co-author graph based on institutional affiliations. I have a list of authors (or even a list of pubmed IDs) and thought I'd simply go to Pubmed and extract affili ...
network written 5.1 years ago by xanderpico150 • updated 4.8 years ago by Pierre Lindenbaum110k

Latest awards to xanderpico

Scholar 6 weeks ago, created an answer that has been accepted. For A: expression to networking
Scholar 9 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: expression to networking
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Informatics On Biologists: Author Affiliations
Student 5.1 years ago, asked a question with at least 3 up-votes. For Informatics On Biologists: Author Affiliations

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