User: xanderpico
xanderpico • 150
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Posts by xanderpico
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... 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
xanderpico • 150
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... 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
xanderpico • 150
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... 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
xanderpico • 150
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... 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
xanderpico • 150
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... 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
xanderpico • 150
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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
xanderpico • 150
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... 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
xanderpico • 150
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... 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
xanderpico • 150
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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
xanderpico • 150
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... 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 ...
written 5.1 years ago by
xanderpico • 150
• updated
4.8 years ago by
Pierre Lindenbaum ♦ 110k
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