User: scooter
scooter • 370
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Posts by scooter
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... Unfortunately, we don't support vertical labels.
-- scooter ...
written 16 days ago by
scooter • 370
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... Greetings,
In order to use BiNGO for a non-model species, you actually need two files -- an *annotation* file, which indicates which terms each gene has, and an *ontology* file, which represents a hierarchy of terms. You can't convert an annotation file into an ontology file since it doesn't conta ...
written 4 weeks ago by
scooter • 370
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... As you point out, that App hasn't been updated in quite a while. I would suggest reaching out to the authors (click the E-Mail button on the App Store page for the App) and see what might be happening. I loaded the App and I don't see the "Search" button, but I would imagine you would have to do C ...
written 5 weeks ago by
scooter • 370
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... Offhand, I would guess that for some reason that column was imported as a string column, not a floating point column. That can happen if your p-value column has N/A or < 0.5 or other non-numeric annotations.
-- scooter
...
written 5 weeks ago by
scooter • 370
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... Ugh. Yes, that got forgotten when the new analyzer was written. You can do the same thing with clusterMaker. Do an Apps->clusterMaker->Connected components cluster. That will add a column called "__ccCluster" that contains the component number of each connected component.
-- scooter ...
written 6 weeks ago by
scooter • 370
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... Sorry -- yes the tutorial web site moved and the jActiveModules got missed. I'll bring that up on our next call. As far as not seeing the results panel, is the results panel empty or is it not showing up at all? If it's not showing up at all, you can bring it up manually by doing View->Show Re ...
written 7 weeks ago by
scooter • 370
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... If I had to guess, those look like identifiers and aren't meaningful in any way as an indication of the evidence (i.e., they are not meant to be a score). I would suggest e-mailing the authors to see if they can provide you with any additional information.
--- scooter ...
written 7 weeks ago by
scooter • 370
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... If you want to change the confidence limits of the STRING network, there are a couple ways to do that. First, you can switch the confidence limit by using the menu Apps->STRING->Change confidence. This will remove edges that don't meet your new confidence cutoff. A better way to explore th ...
written 7 weeks ago by
scooter • 370
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... Hi Nina,
I'm not sure what settings you are looking for, but the initial query and cutoffs are preserved for protein queries. The confidence score and the species are saved in the network table, and the terms that were queried are saved in the node table in the column "query term". Does that h ...
written 7 weeks ago by
scooter • 370
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... Are you trying to install ClueGO? If so, there have been some reports of issues installing apps that appear to have been resolved. Can you give the installation another try? ...
written 9 weeks ago by
scooter • 370
Latest awards to scooter
Scholar
3 months 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?
Scholar
6 months ago,
created an answer that has been accepted.
For A: How to show selected node lables only in cytoscape?
Scholar
6 months ago,
created an answer that has been accepted.
For A: How to show selected node lables only in cytoscape?
Scholar
11 months ago,
created an answer that has been accepted.
For A: How to show selected node lables only in cytoscape?
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: Nteworks in Cytoscape, time-series gene-expression
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