Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: xanderpico

gravatar for xanderpico
xanderpico • 170
Reputation:
170
Status:
Trusted
Location:
Last seen:
1 month, 1 week ago
Joined:
6 years, 8 months ago
Email:
x*********@gmail.com

about me

Posts by xanderpico

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
168
views
0
answers
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 xanderpico • 170
0
votes
1
answer
170
views
1
answers
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 xanderpico • 170
0
votes
1
answer
1.2k
views
1
answers
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 xanderpico • 170
1
vote
2
answers
381
views
2
answers
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 xanderpico • 170
1
vote
2
answers
504
views
2
answers
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 xanderpico • 170
0
votes
1
answer
834
views
1
answers
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 xanderpico • 170
0
votes
1
answer
834
views
1
answers
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 xanderpico • 170
2
votes
1
answer
478
views
1
answers
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 xanderpico • 170
1
vote
1
answer
821
views
1
answers
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 xanderpico • 170
1
vote
1
answer
2.2k
views
1
answers
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 xanderpico • 170

Latest awards to xanderpico

Scholar 12 months ago, created an answer that has been accepted. For A: expression to networking
Scholar 21 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: expression to networking
Popular Question 6.0 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 6.0 years ago, created a question with more than 1,000 views. For Informatics On Biologists: Author Affiliations
Student 6.0 years ago, asked a question with at least 3 up-votes. For Informatics On Biologists: Author Affiliations
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2118 users visited in the last hour