User: bernatgel
bernatgel • 2.6k
- Reputation:
- 2,600
- Status:
- Trusted
- Location:
- Barcelona, Spain
- Twitter:
- @bernatgel
- Last seen:
- 2 days, 5 hours ago
- Joined:
- 6 years, 3 months ago
- Email:
- b********@gmail.com
about me
Posts by bernatgel
<prev
• 153 results •
page 1 of 16 •
next >
0
votes
0
answers
57
views
0
answers
... Hi curious,
In my experience, biology and real data are usually muuuuuch more complex than most simulations and there will always be sources of variation you won't take into account that will impact you results. If possible, I'd suggest you trying to find at least a few positive and negative exampl ...
written 3 days ago by
bernatgel • 2.6k
3
votes
1
answer
105
views
1
answers
... Hi @gabi,
When karyoploteR creates the ideogram but nothing gets added to it with the other plotting functions, in many cases it is due to different chromosome names.
Are your gr chromosome names in UCSC style ("chr1", "chr2", ...) or in Ensembl/NCBI style ("1", "2", ...)? The default bioconduct ...
written 23 days ago by
bernatgel • 2.6k
0
votes
3
answers
2.8k
views
3
answers
... If you would be also happy with non-circular plot, you can try with [karyoploteR](http://bioconductor.org/packages/karyoploteR). It's an R/Bioconductor package and it should be easier to grasp than circos config files.
As Circos, it can represent any data type, including ChIP-seq data and you can z ...
written 5 weeks ago by
bernatgel • 2.6k
0
votes
0
answers
88
views
0
answers
Comment:
C: Qustion about Circos Plot
... I cannot see the image, but what I can understand from the text is that:
1 - You need to have the indels already computed and know the genomic position of each one
2 - Then, divide the genome into 1Mb windows (possibly overlapping)
3 - For each 1Mb region of your genome, count the number of in ...
written 5 weeks ago by
bernatgel • 2.6k
2
votes
1
answer
633
views
1
answers
... You can create images like that with [karyoploteR](https://bioconductor.org/packages/karyoploteR/), an R/Bioconductor package.
In the [karyoploteR tutorial page](https://bernatgel.github.io/karyoploter_tutorial//Examples/EncodeEpigenetics/EncodeEpigenetics.html) you can find the step-by-step explan ...
written 5 weeks ago by
bernatgel • 2.6k
1
vote
0
answers
127
views
0
answers
Comment:
C: Genes on chromosome
... If you want to try karyoploteR, you can find a tutorial page with the code you need at https://bernatgel.github.io/karyoploter_tutorial//Examples/PlotGenes/PlotGenes.html ...
written 5 weeks ago by
bernatgel • 2.6k
0
votes
0
answers
98
views
0
answers
... Hi,
I started working on a package for this kind of plots based in karyoploteR a year ago, but I had to pause its development. It's still in the early stages, but it kind of works already. You can take a look at https://github.com/bernatgel/genoploteR ...
written 3 months ago by
bernatgel • 2.6k
0
votes
1
answer
158
views
1
answers
... Hi @Rubai,
The list has one GRanges per chromosome. You unlist approach is valid.
Also yes, the mutations that it returns are the ones that are closer to 1kb to the NEXT mutation. In some cases missing the last mutation of a cluster of several mutations could be acceptable. If you want them you co ...
written 4 months ago by
bernatgel • 2.6k
2
votes
1
answer
158
views
1
answers
... Hi Rubai,
If you are already using `kpPlotRainfall` you can take advatage of the distances it computes. You should call it and assign the result to kp again
kp <- kpPlotRainfall(kp, data=your.data, [...])
and then you can get the distances with
distances <- kp$latest.plot$computed. ...
written 4 months ago by
bernatgel • 2.6k
0
votes
2
answers
4.3k
views
2
answers
... This can be easily done with [karyoploteR](https://bioconductor.org/packages/karyoploteR/). It can deal directly with [BigWig files](https://bernatgel.github.io/karyoploter_tutorial//Examples/EncodeEpigenetics/EncodeEpigenetics.html) or plot [any data that can be loaded into R](https://bernatgel.git ...
written 4 months ago by
bernatgel • 2.6k
Latest awards to bernatgel
Teacher
20 days 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
20 days ago,
created an answer that has been accepted.
For A: How to convert mutation position from gene coordinate to genome coordinate?
Teacher
4 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
Scholar
4 months ago,
created an answer that has been accepted.
For A: How to convert mutation position from gene coordinate to genome coordinate?
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Appreciated
7 months ago,
created a post with more than 5 votes.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
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
Teacher
8 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
9 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Teacher
9 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
Great Question
9 months ago,
created a question with more than 5,000 views.
For karyoploteR: uncircle your genomes
Scholar
10 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Good Answer
13 months ago,
created an answer that was upvoted at least 5 times.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher
13 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
14 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
14 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Scientific Programmer for Translational Bioinformatics of Hereditary Cancer at the IMPPC, Badalona, Barcelona, Spain
Centurion
14 months ago,
created 100 posts.
Appreciated
16 months ago,
created a post with more than 5 votes.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Appreciated
17 months ago,
created a post with more than 5 votes.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Scholar
17 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Good Answer
17 months ago,
created an answer that was upvoted at least 5 times.
For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher
17 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
17 months ago,
created an answer that has been accepted.
For A: Testing for over-representation of chip-peaks
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1646 users visited in the last hour