User: bernatgel

gravatar for bernatgel
bernatgel770
Reputation:
770
Status:
Trusted
Location:
Barcelona, Spain
Twitter:
@bernatgel
Last seen:
1 day, 1 hour ago
Joined:
3 years, 5 months ago
Email:
b********@gmail.com

about me

Posts by bernatgel

<prev • 45 results • page 1 of 5 • next >
0
votes
2
answers
193
views
2
answers
Answer: A: circos plot gene expression by RNA-Seq
... If you don't mind it not being round, you could use the [R/Bioconductor package](http://bioconductor.org/packages/devel/bioc/html/karyoploteR.html) called [karyoploteR](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx346) to represent differential expression data ...
written 14 days ago by bernatgel770
1
vote
1
answer
333
views
1
answers
Answer: A: RNA seq Newbie needing help
... Performing an experiment with 576 samples without at least a small pilot seems quite risky. At least to check that there are some changes and that you can find the what you would clearly expect. I think something like a pilot with two tanks, 2 time points (0 and 7), 2/3 fish per tank and a single ...
written 21 days ago by bernatgel770
0
votes
3
answers
269
views
3
answers
Comment: C: Localise up-regulated & down-regulated genes across the genome
... You can find [an example](https://bernatgel.github.io/karyoploter_tutorial//Examples/GeneExpression/GeneExpression.html) that might be helpful in karyoploteR's [Examples and Tutorial](https://bernatgel.github.io/karyoploter_tutorial/) site. It has complete code to get to something very similar to wh ...
written 23 days ago by bernatgel770
0
votes
2
answers
162
views
2
answers
Answer: A: amplicon based germline CNV caller
... I have no direct experience with any of them, but there are a few tools available for that. Some of them talk about targeted sequencing but do not specify if they would work for amplicons or only for hybridization based data. Most of them are designed to work with germinal data, since they are aimed ...
written 4 weeks ago by bernatgel770
0
votes
2
answers
322
views
2
answers
Comment: C: How to draw the chromosome specific coverage plot using GFF3 file
... Hi @ajaybioinfo, In your code, when you create the custom genome, you have two starts and only one chromosome. This creates an invalid genome (with two chromosomes of the same name) and prevent kpPlotDensity from working. This should work library(karyoploteR) custom.genome <- toGRange ...
written 4 weeks ago by bernatgel770
0
votes
4
answers
336
views
4
answers
Comment: C: How to map SNPs of C. Albicans using custom data?
... Hi, Are you using the development version (it needs the development version of Bioconductor). The rainfall plot is only available in the development version right now and will be in release with the next Bioconductor release ( ~ October 2017). To use it you should install Bioconductor devel (you ha ...
written 6 weeks ago by bernatgel770
0
votes
4
answers
336
views
4
answers
Comment: C: How to map SNPs of C. Albicans using custom data?
... Hi @nattzy94, Right now only two data panels are implemented: one above and one below the chromosome. However all of them can be partitioned to plot more than one data "track" with the parameters r0 and r1 (you can find more information on the [Data Postioning tutorial](https://bernatgel.github. ...
written 7 weeks ago by bernatgel770
0
votes
2
answers
322
views
2
answers
Comment: C: How to draw the chromosome specific coverage plot using GFF3 file
... Hi @ajaybioinfo, I've replied to the email you sent me. Here's the reply If you want to add some tracks with density data in the format you have given, you will only need to load that data into R and plot it with kpPlotDensity. Please follow these steps: 1 - Load all your data into R. You can ...
written 7 weeks ago by bernatgel770
2
votes
2
answers
217
views
2
answers
Answer: A: Add a legend to circos plot
... As far a I know, there is no functionality in Circos to add labels to tracks. We usually use an external program (Inskscape or similar) to add the labels when preparing the figure to publish. Another option would be to use a text track with the track names, and try to position them as if they were ...
written 9 weeks ago by bernatgel770
0
votes
4
answers
336
views
4
answers
Comment: C: How to map SNPs of C. Albicans using custom data?
... I edited the original answer to include some code ...
written 9 weeks ago by bernatgel770

Latest awards to bernatgel

Librarian 10 days ago, created a post with more than 10 bookmarks. For karyoploteR: uncircle your genomes
Scholar 9 weeks ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Prophet 9 weeks ago, created a post with more than 20 followers. For karyoploteR: uncircle your genomes
Voter 12 weeks ago, voted more than 100 times.
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated 3 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 3 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated 3 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 6 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Supporter 15 months ago, voted at least 25 times.
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Scholar 2.1 years ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Association between bed files - statistical significance

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1463 users visited in the last hour