User: justp

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justp10
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Posts by justp

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Comment: C: Gene set enrichment analysis vs functional enrichment analysis?
... Where can I find these GSEA options for other databases. I'm trying to do some analysis with a list of genes that I have read are involved in a pathway, but I don't have expression data from any experiments. ...
written 20 months ago by justp10
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Gene set enrichment analysis vs functional enrichment analysis?
... I'm confused about what these two are. I saw functional enrichment analysis being used to describe when someone takes a gene list and runs it through DAVID and GSEA being referred to as functional enrichment analysis. I thought you needed your own expression data to do GSEA, how does DAVID work t ...
david gsea functional enrichment analysis written 20 months ago by justp10 • updated 20 months ago by jared.andrews072.7k
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Comment: C: Automated layout algorithms for cellular pathways?
... Thank you for the suggestion. I've looked at the DOT format, but it seems that I would have to manually type out everything or either create a script for Excel that writes everything into the DOT format. I'm not sure how this solves my problem, unless there's some algorithm I can implement using the ...
written 24 months ago by justp10
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Creating a network in Cytoscape with nodes that have the same name
... I'm using Excel to compile genes involved in a pathway, that I'm getting from literature. I figured out that I can import an Excel file into Cytoscape to show interactions between different nodes. What I've essentially done is assign each node a separate number and this allows me to have interaction ...
pathway network cytoscape written 24 months ago by justp10 • updated 24 months ago by solo777370
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Comment: C: Editing and saving KEGG pathway files
... Thanks! Just wanted to update this. There is information that is likely hard coded in the PNG file or whatever that isn't coded in the xml file, so there is some information that is visible on the image found in the PNG file on the KEGG website, but isn't in the xml file. I've tried what you said an ...
written 2.0 years ago by justp10
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Comment: C: KGML missing information and visualization issues with Cytoscape
... Thank you. That's what I assumed. I was hoping there was a more machine readable file that the KEGG database had in addition to the accessible xml file, but I'm guessing that doesn't exist or isn't available. ...
written 2.0 years ago by justp10
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Automated layout algorithms for cellular pathways?
... I'm new to bioinformatics. I'm trying to learn more about algorithms that are used for pathway layouts and how that works. For example if one has an xml, gpml, or csv files with gene names and attributes (including cellular location) and interaction (gene1 activates gene2), but not specific node loc ...
pathway layout written 2.0 years ago by justp10 • updated 2.0 years ago by Jean-Karim Heriche20k
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KGML missing information and visualization issues with Cytoscape
... I'm having difficulties viewing KEGG pathways properly in Cytoscape. There's missing information in the XML file that prevents Cytoscape from displaying certain relationships and annotations. Is this something that is just unavoidable? How does KEGG display pathway related information like how a ce ...
kegg cytoscape written 2.1 years ago by justp10 • updated 2.0 years ago by Keiichiro Ono130
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Editing and saving KEGG pathway files
... I wanted to know if there is a way to take xml files from KEGG and be able to add proteins in a pre-existing group in the pathway, then save that in a new xml file that retains the existing xml information with the new changes. I've been running into trouble with being able to save the xml files usi ...
xml kegg cytoscape written 2.3 years ago by justp10 • updated 2.3 years ago by theobroma221.1k

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