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User: xanderpico

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xanderpico • 330
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Posts by xanderpico

<prev • 43 results • page 1 of 5 • next >
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Answer: A: Diseases related pathways
... The [rWikiPathways package in bioconductor][1] lets you search the database in a few different ways. Like the comments above, exactly how *you* define a "diabetes pathway" is up to you. For example, you can search for any pathway that mentions "diabetes" anywhere in the title or description and then ...
written 6 days ago by xanderpico • 330
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Answer: A: Kegg annotation for gene
... As an alternative to KEGG, the rWikiPathways package in Bioconductor makes this easy: https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html. Once you've installed the package, then you can search by gene symbols (e.g., HGCN symbols) such "TNF" and get a dataframe listing pathways by ...
written 29 days ago by xanderpico • 330
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Comment: C: Obtaining directionality of pathways
... For WikiPathways, there is also a Cytoscape app[1] that lets you import pathways as directed networks. This can all be controlled from R via the RCy3 package[2]. 1. http://apps.cytoscape.org/apps/wikipathways 2. https://bioconductor.org/packages/release/bioc/html/RCy3.html ...
written 6 weeks ago by xanderpico • 330
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Answer: A: How Can I plot this data in a heatmap?
... If I had data in that format, I would import it into Cytoscape and view it as a network of pathway and uniprot nodes. A force-directed layout would immediately reveal pathways that share a lot of proteins in common, as well as proteins that are common across lots of pathways, etc. But, ultimately, ...
written 7 weeks ago by xanderpico • 330
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Comment: C: Analysis of GSE dataset in Cytoscape
... Cytoscape can import any sort of tabular dataset. The challenge is matching the steps with your analysis goals. So, more information is needed in order to help. For example, if you have a network loaded in Cytoscape and you want to import GSE data, then you simply need to have the data in a tabular ...
written 10 weeks ago by xanderpico • 330
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Answer: A: Protein-Protein interaction (Cytoscape)
... There is an app for that: http://apps.cytoscape.org/apps/networkrandomizer. The associated paper may be helpful as well: https://f1000research.com/articles/5-2524/v3 ...
written 12 weeks ago by xanderpico • 330
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Comment: C: MCODE cytoscape analysis
... You may have seen these already, but there are tutorial and documentation links from both the MCODE app and clusterMaker2 apps, which can each perform MCODE clustering: - http://apps.cytoscape.org/apps/mcode - http://apps.cytoscape.org/apps/clustermaker2 If you are asking about MCODE clustering ...
written 12 weeks ago by xanderpico • 330
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Answer: A: Gene list pathway classification and visualization
... There are indeed a lot of tools and resources to choose from. Three important considerations are (1) methods, (2) update frequency, and (3) coverage. 1. METHODS. The methods for pathways classification you are asking about are generally refered to as functional enrichment analyses and include over- ...
written 12 weeks ago by xanderpico • 330
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Comment: C: Drawing KEGG-type metabolic pathways
... [WikiPathways](https://wikipathways.org) are available in SVG. These are updated each month based on community curation: http://data.wikipathways.org/current/svg/. If you make new pathways (or improved versions of existing pathways) in PathVisio, you can then save them back to WikiPathways and shar ...
written 3 months ago by xanderpico • 330
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Answer: A: Pathways Analysis in R
... There are [a lot of options](https://www.bioconductor.org/packages/release/BiocViews.html#___GeneSetEnrichment). Here are a couple specific recommendations: - [clusterProfiler](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html) - actively maintained R package with great docu ...
written 3 months ago by xanderpico • 330

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