Moderator: geek_y
geek_y ♦ 10k
- Reputation:
- 10,110
- Status:
- Trusted
- Location:
- Barcelona
- Twitter:
- geek_y
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 hours ago
- Joined:
- 7 years, 11 months ago
- Email:
- g***********@gmail.com
I work with range of genomics data like transcriptome (RNA-Seq, scRNA-Seq, CAGE-Seq), open-chromatin/histone modifications/TF profiles, chromosome contact maps etc to understand tissue specific transcriptional regulation in human genome w.r.t to T2D.
I also work on small part of genetics (eQTLs, caQTLs, hQTLs etc) to understand role of common genetic variants in genome regulation.
Posts by geek_y
<prev
• 1,434 results •
page 1 of 144 •
next >
0
votes
1
answer
135
views
1
answers
Comment:
C: SC-RNA Seq Analysis tutorials
... very useful information. ...
written 3 months ago by
geek_y ♦ 10k
0
votes
0
answers
113
views
0
answers
... Are you talking about Transcriptome Wide Association Studies ? What softwares are you talking about ? No. of samples for each SNP ? Or the sample size required to perform TWAS ? ...
written 3 months ago by
geek_y ♦ 10k
3
votes
1
answer
133
views
1
answers
... One option is to use the samples with only non-zero expression values. Other option is to perform permutations and calculate a p-value. ...
written 3 months ago by
geek_y ♦ 10k
0
votes
0
answers
113
views
0
answers
... What do you mean by N ? ...
written 3 months ago by
geek_y ♦ 10k
0
votes
1
answer
204
views
1
answers
... I am aware only of [JTKCycle][1] for identifying cycling genes.
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119870/ ...
written 3 months ago by
geek_y ♦ 10k
0
votes
1
answer
154
views
1
answers
... GTEx provides [exon-exon junction counts][1] if that helps.
[1]: https://gtexportal.org/home/datasets#filesetFilesDiv13 ...
written 3 months ago by
geek_y ♦ 10k
2
votes
3
answers
164
views
3
answers
... If you don't know batches, may be RUVSeq helps but it depends on non-differential gene expression to estimate surrogate variables. PCA regression performs well. Its included not in sva package as [sva_network][1] function. Plot the PCs and see how many PCs to regress out. sva also has function to es ...
written 3 months ago by
geek_y ♦ 10k
2
votes
3
answers
264
views
3
answers
... Super enhancer are nothing but collection of closely spaced individual "peaks" (less than 12.5kb I guess) in linear genomic space. So if you want to do a differential analysis, you could just perform a differential binding of all individual peaks and show an enrichment of differential peaks being a ...
written 3 months ago by
geek_y ♦ 10k
1
vote
1
answer
221
views
1
answers
Answer:
A: SNP calling and SNP discovery
... https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 ...
written 4 months ago by
geek_y ♦ 10k
0
votes
1
answer
682
views
1
answers
... You can add your own answer what you think is the best for the question. I said it doesn't perform terrible. I did not say its the best.
Here is a plot which I generated using total count normalisation and the cells cluster by cell-types. Ofcourse, normalisation methods developed especially for sc ...
written 4 months ago by
geek_y ♦ 10k
Latest awards to geek_y
Great Question
8 days ago,
created a question with more than 5,000 views.
For Multisample VCF file to Structure file format ?
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Great Question
9 weeks ago,
created a question with more than 5,000 views.
For Multisample VCF file to Structure file format ?
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Good Answer
11 weeks ago,
created an answer that was upvoted at least 5 times.
For A: How get intervals of low coverage from a genome sequence?
Commentator
3 months ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Scholar
3 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
3 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Great Question
4 months ago,
created a question with more than 5,000 views.
For Multisample VCF file to Structure file format ?
Scholar
4 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Scholar
4 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Cylon
5 months ago,
received 1,000 up votes.
Appreciated
5 months ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Appreciated
7 months ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Scholar
8 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Appreciated
8 months ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1939 users visited in the last hour