User: bernatgel

gravatar for bernatgel
bernatgel2.6k
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
Comment: C: Simulating whole gene deletions for tuning a WES based CNV calling approach?
... 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 bernatgel2.6k
3
votes
1
answer
105
views
1
answers
Answer: A: How to plot genomic regions using KaryoplotR
... 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 bernatgel2.6k
0
votes
3
answers
2.8k
views
3
answers
Answer: A: CIRCOS plot with Chip-Seq Data
... 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 bernatgel2.6k
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 bernatgel2.6k
2
votes
1
answer
633
views
1
answers
Answer: A: What tools I should use to make such a bioinformatic picture?
... 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 bernatgel2.6k
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 bernatgel2.6k
0
votes
0
answers
98
views
0
answers
Comment: C: Plot transcripts with exaggerated exons and very short introns in R
... 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 bernatgel2.6k
0
votes
1
answer
158
views
1
answers
Comment: C: Find mutations that are spatially clustered?
... 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 bernatgel2.6k
2
votes
1
answer
158
views
1
answers
Answer: A: Find mutations that are spatially clustered?
... 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 bernatgel2.6k
0
votes
2
answers
4.3k
views
2
answers
Answer: A: Plotting chromosomal data from sliding window analyses
... 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 bernatgel2.6k

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?
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
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
Centurion 14 months ago, created 100 posts.
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

Help
Access

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