User: scooter
scooter • 200
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Posts by scooter
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... Answered on the Cytoscape helpdesk here: https://groups.google.com/forum/?hl=en_US/#!topic/cytoscape-helpdesk/TD-L4boryn0
-- scooter
...
written 9 days ago by
scooter • 200
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... Sorry, I don't know of any database that includes mRNA-small molecule interactions.
-- scooter ...
written 9 days ago by
scooter • 200
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Answer:
A: DissTOM and Cytoscape - WGCNA
... Hi Silvia,
WGCNA uses the dissimilarity matrix from the topological overlap matrix to reduce the effects of noise and spurious associations (from the manual), before doing the hierarchical clustering.
As to your second question, probably the easiest way to get from igraph in R to Cytoscape ...
written 9 days ago by
scooter • 200
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... First, there isn't much documentation on the home page. I would strongly suggest going to tutorials.cytoscape.org and going through some of the tutorials there.
Second, as to your specific question: edges don't have a Z-order, so you can't modify the order of an edge. On the other hand, if your n ...
written 9 days ago by
scooter • 200
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... As the previous comment suggested, you need to first figure out what your question is. For example, say your g-B column represents a condition fold change and your g-E column represents some treatment condition fold change. And you're interested in seeing what terms best describe the genes where g ...
written 9 days ago by
scooter • 200
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... Unfortunately, none of the apps I was able to find deduce the edges between the species in the KEGG pathway. I looked at the KGML and, as near as I can tell, the actual links aren't encoded in the file. That pathway has a list of gene, some relatively long labels for the genes (see the tag) and t ...
written 16 days ago by
scooter • 200
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... Well, there are two ways to think about grouping. First, grouping a set of nodes into a compound node can help visualize some distinct aspect of those nodes. For example, a group of proteins might form a complex. Second, in very dense networks, you may want to abstract a set of nodes and collaps ...
written 17 days ago by
scooter • 200
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... Have you tried looking at the LegendCreator app? That should give you a visual ramp that includes the values and the corresponding values from your Edge table.
-- scooter
...
written 17 days ago by
scooter • 200
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... The "right" answer here is: "it depends". 600 nodes and 2000 edges is not a very large network, depending on what you are trying to show. For example, this image of yeast genetic interactions has ~4000 nodes:
![Yeast Genetic Interaction Network][1].
If you are trying to show a pathway and see ...
written 23 days ago by
scooter • 200
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... Hi,
The easiest way is to simply copy the style and make your changes in the new style. Look at the little menu just to the left of the style name in the style tab. You should be able to copy the style, give it a new name, and then switch to that style for your second network.
Hope that helps! ...
written 24 days ago by
scooter • 200
Latest awards to scooter
Scholar
16 days ago,
created an answer that has been accepted.
For A: How to show selected node lables only in cytoscape?
Scholar
23 days ago,
created an answer that has been accepted.
For A: How to show selected node lables only in cytoscape?
Scholar
5 months ago,
created an answer that has been accepted.
For A: How to show selected node lables only in cytoscape?
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: Nteworks in Cytoscape, time-series gene-expression
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