User: scooter
scooter • 80
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Posts by scooter
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... Hi,
Definitely, you can set up a discrete mapper and then you can right-click and select "Mapping Value Generators" and choose one of the generators. Note that 18 different colors is probably too many for a user to distinguish, but it might be useful for exploration.
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written 10 days ago by
scooter • 80
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... I'm not sure I can answer the question of "validity" with just the description you've given us. Some additional information might help:
1. It sounds like you are creating a bi-partide network, with food classes as one type of node and gene-targets as another. Is that right?
2. I'm not clear how ...
written 10 weeks ago by
scooter • 80
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... Hi Michael,
Do you mean export a set of currently selected nodes and their interactions? As you stated, SIF will give you a table of all nodes and their partners. If you want specific nodes and their partners, what I would do is to select the nodes you want to include, select all of the first n ...
written 10 weeks ago by
scooter • 80
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... An alternative to what Devon mentioned is to use the Cytoscape App Manager and install stringApp from there. Just go to Apps->App Manager and you can find the stringApp and install it. Alternatively, since you've already downloaded it, you can do an "install from file" from within the App Manag ...
written 5 months ago by
scooter • 80
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... In general, the cluster numbers are roughly ordered from largest cluster to smallest cluster, but each algorithm might treat these somewhat differently. Not sure why GLay isn't just ordering the clusters like other algorithms (e.g. MCL) do.
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written 5 months ago by
scooter • 80
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... I think you need to add the CluePedia app to do that.
-- scooter
...
written 7 months ago by
scooter • 80
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... Greetings,
Sure here you go:
1. add the stringApp to Cytoscape 3.7.0
2. in the Network panel search bar, select STRING Protein Query
3. paste your genes of interest into the text box. Note that you should probably filter your gene list to those that show significant fold change and p-Value
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written 7 months ago by
scooter • 80
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... What public database service are you using? I've been using STRING (through stringApp) a lot lately and it's been working fine for me. ...
written 7 months ago by
scooter • 80
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... Hi Malgosia,
Importing the data shouldn't be a problem. Each of your conditions would be a separate column, and you can color the nodes by the expression value in that column. Pathway enrichment would be a little trickier, but fundamentally just the same basic steps repeated over and over:
1. ...
written 10 months ago by
scooter • 80
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... What version of Cytoscape are you using? There was certainly a problem with previous versions not deleting rows/nodes in the root network, but I think it should be *much* better now.
-- scooter ...
written 10 months ago by
scooter • 80
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10 months ago,
created an answer with at least 3 up-votes.
For A: Nteworks in Cytoscape, time-series gene-expression
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