User: xanderpico
xanderpico • 160
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Posts by xanderpico
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... Sure! You can paste you gene names into the Network Search Bar (upper left). If you have the stringApp or GeneMANIA apps installed, they'll be added to this same interface and you can directly search them the same way from within Cytoscape. Here's the manual page:
http://manual.cytoscape.org/en/sta ...
written 23 days ago by
xanderpico • 160
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... I haven't used jactivemodules in years, but it seems like the tutorial linked to from the Cytoscape App Store page answers your questions...
http://apps.cytoscape.org/apps/jactivemodules --> http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:JActiveModules_3
1. Yes, it works with a combination ...
written 3 months ago by
xanderpico • 160
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... Hi. There are a few directions you could go with your analysis of expression data in Cytoscape. The first step in most cases is to identify the source of the network or pathway that you want to work with. Unfortunately, there is not a single "true" network :). Souces include:
- [NDEx][1] - for use ...
written 3 months ago by
xanderpico • 160
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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 5 months ago by
xanderpico • 160
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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 7 months ago by
xanderpico • 160
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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 8 months ago by
xanderpico • 160
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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 months ago by
xanderpico • 160
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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 9 months ago by
xanderpico • 160
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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 10 months ago by
xanderpico • 160
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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 11 months ago by
xanderpico • 160
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