User: xanderpico
xanderpico • 330
- 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
xanderpico • 330
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
xanderpico • 330
0
votes
0
answers
127
views
0
answers
... 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
1
vote
1
answer
175
views
1
answers
... 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
0
votes
0
answers
177
views
0
answers
... 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
2
votes
1
answer
185
views
1
answers
... 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
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
xanderpico • 330
4
votes
1
answer
170
views
1
answers
... 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
0
votes
1
answer
351
views
1
answers
... [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
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
xanderpico • 330
Latest awards to xanderpico
Popular Question
7.5 years ago,
created a question with more than 1,000 views.
For Software Engineer To Work On Crowdsourcing Tools For Biomedical Research Org In San Francisco
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
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