User: xanderpico

gravatar for xanderpico
xanderpico290
Reputation:
290
Status:
Trusted
Location:
Last seen:
1 day, 6 hours ago
Joined:
7 years, 12 months ago
Email:
x*********@gmail.com

about me

Posts by xanderpico

<prev • 38 results • page 1 of 4 • next >
2
votes
1
answer
61
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 1 day ago by xanderpico290
0
votes
0
answers
38
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 1 day ago by xanderpico290
4
votes
1
answer
66
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 3 days ago by xanderpico290
0
votes
1
answer
220
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 20 days ago by xanderpico290
0
votes
1
answer
221
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 20 days ago by xanderpico290
1
vote
2
answers
188
views
2
answers
Answer: A: Extract Pathway Topological Graphs (With Metabolites) from Reactome and WikiPath
... Reactome and WikiPathways both have apps for Cytoscape that pull their content into a graph model: - [ReactomeFI plugin](http://apps.cytoscape.org/apps/reactomefiplugin) - [WikiPathways app](http://apps.cytoscape.org/apps/wikipathways) In the case of the WikiPathways app, you have the explicit o ...
written 20 days ago by xanderpico290
0
votes
0
answers
171
views
0
answers
Comment: C: Cluepedia 'create custom file' option not working on MacBook and cytoscape keeps
... The app authors for ClueGO have been great at replying to email questions. Not sure if they are following questions here, however. Their contact info is on their app page: apps.cytoscape.org/apps/cluego ...
written 3 months ago by xanderpico290
0
votes
1
answer
176
views
1
answers
Answer: A: Enrichment analysis using Clusterprofiler R/Cytoscape
... There may be multiple approaches, but here is how I do that sort of analysis: 1. Translate your identifiers to NCBI Gene (Entrez) IDs using the `bitr` function (as described in clusterProfiler tutorial). 2. Use your prefered `apply` to run `enricher` on each of your module gene sets. The function ...
written 3 months ago by xanderpico290
1
vote
2
answers
190
views
2
answers
Answer: A: Importing Newick trees in Cytoscape by conversion to igraph via RCy3
... It looks like you've changed the line. The original is: tree <- phytools::read.newick(system.file("extdata","phylotree.newick", package="RCy3")) Which is grabbing an example newick file provided by the RCy3 package. You've replaced with filename with a local path, which obviously is not a p ...
written 3 months ago by xanderpico290
0
votes
0
answers
145
views
0
answers
Comment: C: The question about the Cytohubba
... I don't know if the app authors track questions here or not, but you can find their email contact info on their app page: https://apps.cytoscape.org/apps/cytohubba ...
written 3 months ago by xanderpico290

Latest awards to xanderpico

Scholar 3 days ago, created an answer that has been accepted. For A: expression to networking
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: expression to networking
Scholar 10 months ago, created an answer that has been accepted. For A: expression to networking
Scholar 2.4 years ago, created an answer that has been accepted. For A: expression to networking
Scholar 3.1 years ago, created an answer that has been accepted. For A: expression to networking
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: expression to networking
Popular Question 7.3 years ago, created a question with more than 1,000 views. For Informatics On Biologists: Author Affiliations
Student 7.3 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: 851 users visited in the last hour