User: xanderpico

gravatar for xanderpico
xanderpico330
Reputation:
330
Status:
Trusted
Location:
Last seen:
6 days, 13 hours ago
Joined:
8 years, 2 months ago
Email:
x*********@gmail.com

about me

Posts by xanderpico

<prev • 43 results • page 1 of 5 • next >
2
votes
2
answers
120
views
2
answers
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 xanderpico330
1
vote
2
answers
166
views
2
answers
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 xanderpico330
0
votes
0
answers
127
views
0
answers
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 xanderpico330
1
vote
1
answer
175
views
1
answers
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 xanderpico330
0
votes
0
answers
177
views
0
answers
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 xanderpico330
2
votes
1
answer
185
views
1
answers
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 xanderpico330
0
votes
0
answers
305
views
0
answers
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 xanderpico330
4
votes
1
answer
170
views
1
answers
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 xanderpico330
0
votes
1
answer
351
views
1
answers
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 xanderpico330
0
votes
1
answer
320
views
1
answers
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 xanderpico330

Latest awards to xanderpico

Scholar 12 weeks ago, created an answer that has been accepted. For A: expression to networking
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: expression to networking
Scholar 13 months ago, created an answer that has been accepted. For A: expression to networking
Scholar 2.6 years ago, created an answer that has been accepted. For A: expression to networking
Scholar 3.3 years ago, created an answer that has been accepted. For A: expression to networking
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: expression to networking
Popular Question 7.5 years ago, created a question with more than 1,000 views. For Informatics On Biologists: Author Affiliations
Student 7.5 years ago, asked a question with at least 3 up-votes. For Informatics On Biologists: Author Affiliations

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2282 users visited in the last hour