User: Lluís R.
Lluís R. • 810
- Reputation:
- 810
- Status:
- Trusted
- Location:
- Spain, Barcelona
- Website:
- http://b101nfo.blogspo...
- Twitter:
- Lluis_Rev
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 hours ago
- Joined:
- 5 years, 1 month ago
- Email:
- l************@gmail.com
I am interested nowadays in microarrays, RNA-Seq and genome annotation, GO and pathways. But my goal are to maximize the useful information of each existing experiment. Now I am committing with Bioconductor, you can follow some of my thought in my blog, or in twitter.
Posts by Lluís R.
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Comment:
C: GO network analysis
... The GO network is fixed, so I understand you want some other type of network. What kind of network do you want? What type of information do you have? ...
written 3 months ago by
Lluís R. • 810
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... The structure of the GO data, makes such a combination difficult: it is designed to have separate structure. However, I would recommend to run the over-representative analysis and then see which genes map to which GO found over-represented in your analysis. That way you could further filter your gen ...
written 3 months ago by
Lluís R. • 810
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... I think it is not possible, as the topology method is based precisely on the differences on the structure of each sub ontology. But why do you want to do this? ...
written 3 months ago by
Lluís R. • 810
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... I think it is as good venue to share your research as other. Perhaps here there are more expert than other forums, so it might be worth it. ...
written 4 months ago by
Lluís R. • 810
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Comment:
C: pathview R package not working
... I think the answers is on the warnings you get:
```
Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
``` ...
written 4 months ago by
Lluís R. • 810
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... Totally true, but that was not the question I was answering, it asked specifically for three packages.
And this is duly noted in the KEGG.db package and in the info of the dataitself. This is due to a change in the KEGG license. One can access to the whole KEGG database using the API though. ...
written 5 months ago by
Lluís R. • 810
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... Wasn't this paper https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2006643 ...
written 5 months ago by
Lluís R. • 810
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Comment:
C: what next after DEGs?
... That depends on your "biological" question and your data. What question do you want to answer? ...
written 5 months ago by
Lluís R. • 810
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... Yes, it is the basic information of the updates of Bioconductor packages. You can find it explained in [Annotation Packages][1]:
> Annotation packages contain lightly or non-curated data from a public source and are updated with each Bioconductor release (every 6 months).
I'll add it in the or ...
written 6 months ago by
Lluís R. • 810
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... Then you need to correct the modgenes variable to the names you want (`nodeNames = rownames(modTOM)[top]`). ...
written 6 months ago by
Lluís R. • 810
Latest awards to Lluís R.
Good Answer
10 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Difference between GO.db, biomaRt, and org.Hs.eg.db in GO annotations
Appreciated
11 weeks ago,
created a post with more than 5 votes.
For A: Difference between GO.db, biomaRt, and org.Hs.eg.db in GO annotations
Scholar
6 months ago,
created an answer that has been accepted.
For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Google Summer Of Code 2014 Gsoc 2014
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Google Summer Of Code 2014 Gsoc 2014
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: StackExchange/Area51 bioinformatics is back
Scholar
15 months ago,
created an answer that has been accepted.
For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Scholar
18 months ago,
created an answer that has been accepted.
For A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
Commentator
22 months ago,
created a comment with at least 3 up-votes.
For C: StackExchange/Area51 bioinformatics is back
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: StackExchange/Area51 bioinformatics is back
Centurion
23 months ago,
created 100 posts.
Voter
2.7 years ago,
voted more than 100 times.
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Which Is An Acceptable Pipeline From Sequencing To Deep Annotation?
Supporter
4.9 years ago,
voted at least 25 times.
Autobiographer
4.9 years ago,
has more than 80 characters in the information field of the user's profile.
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