User: xanderpico

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xanderpico170
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Posts by xanderpico

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Comment: A: How to rank genes on the basis of degree in hubba table in cytoscape
... What's a HubbaTable? I'm guessing it has to do with the CytoHubba app for Cytoscape. If so, you might want to contact the app authors directly. There's a link to their website and email on the app page: http://apps.cytoscape.org/apps/cytohubba ...
written 7 weeks ago by xanderpico170
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Comment: C: Cytoscape - disproportionately big files
... Just a note about an alternative way to reduce .cys files. You can rename them .zip, open them up and remove individual networks (xgmml files), etc., then rezip, and rename. I'd recommend doing this on a copy of your original .cys so you don't permanently wreck an important file :) ...
written 3 months ago by xanderpico170
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Answer: A: How to import a list of gene and visualize gene-gene interaction in Cytoscape ze
... 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 5 months ago by xanderpico170
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Answer: A: How to use Jactivemodule plugin from Cytoscape?
... 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 7 months ago by xanderpico170
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Answer: A: Cytoscape-gene expression data
... 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 7 months ago by xanderpico170
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Answer: A: 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 10 months ago by xanderpico170
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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 11 months ago by xanderpico170
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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 12 months ago by xanderpico170
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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 13 months ago by xanderpico170
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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 13 months ago by xanderpico170

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