User: xanderpico
xanderpico • 150
- Reputation:
- 150
- Status:
- Trusted
- Location:
- Last seen:
- 1 day, 19 hours ago
- Joined:
- 6 years ago
- Email:
- x*********@gmail.com
about me
Posts by xanderpico
<prev
• 17 results •
page 1 of 2 •
next >
0
votes
1
answer
122
views
1
answers
... 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 1 day ago by
xanderpico • 150
0
votes
1
answer
88
views
1
answers
... 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 15 days ago by
xanderpico • 150
0
votes
1
answer
370
views
1
answers
... 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 12 weeks ago by
xanderpico • 150
0
votes
1
answer
370
views
1
answers
... 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 4 months ago by
xanderpico • 150
2
votes
1
answer
247
views
1
answers
... 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 5 months ago by
xanderpico • 150
1
vote
1
answer
407
views
1
answers
... 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 5 months ago by
xanderpico • 150
1
vote
1
answer
1.8k
views
1
answers
... 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 6 months ago by
xanderpico • 150
0
votes
1
answer
373
views
1
answers
... 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 7 months ago by
xanderpico • 150
1
vote
1
answer
325
views
1
answers
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 8 months ago by
xanderpico • 150
0
votes
1
answer
615
views
1
answers
... 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 12 months ago by
xanderpico • 150
Latest awards to xanderpico
Popular Question
5.4 years ago,
created a question with more than 1,000 views.
For Software Engineer To Work On Crowdsourcing Tools For Biomedical Research Org In San Francisco
Popular Question
5.4 years ago,
created a question with more than 1,000 views.
For Informatics On Biologists: Author Affiliations
Student
5.4 years ago,
asked a question with at least 3 up-votes.
For Informatics On Biologists: Author Affiliations
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 855 users visited in the last hour