User: bernatgel

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bernatgel1.2k
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Posts by bernatgel

<prev • 61 results • page 1 of 7 • next >
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Comment: C: karyoploteR: uncircle your genomes
... Hi Vijay, As Bastien said, karyoploteR does not need the reference sequence or anything like that. It just needs the chromosome lengths, which facilitates working with custom and unfinished genomes. I would do something along the lines of what Bastien suggested. 1. Create a GRanges object with ...
written 4 days ago by bernatgel1.2k
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Answer: A: kpPlotLinks function not working in karyoplotR
... Just for future reference, the problem in this case was that the version of [karyoploteR](http://bioconductor.org/packages/karyoploteR/) was an old one, from before the [kpPlotLinks](https://bernatgel.github.io/karyoploter_tutorial/Tutorial/PlotLinks/PlotLinks.html) function was added. The [karyoplo ...
written 5 days ago by bernatgel1.2k
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Answer: A: Is there an available tool to visualize multiple "types" of ChIP-seq peaks on a
... With [karyoploteR](http://bioconductor.org/packages/karyoploteR/) you plot the peaks from the different timepoints in a single "track" creting an overlay. Depending on the format of your data you could either peak intervals with [`kpPlotRegions`](https://bernatgel.github.io/karyoploter_tutorial//Tut ...
written 8 weeks ago by bernatgel1.2k
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Comment: C: Tools for visualization of CNVs called by XHMM
... For an image like this you can also use karyopoteR, but use the [`kpPoints`](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Points/Points.html) function instead of `kpSegments`. You'll need to figure out the values they are plotting (the Z-score it seems) in your output files, load it in ...
written 8 weeks ago by bernatgel1.2k
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Comment: C: Tools for visualization of CNVs called by XHMM
... Hi nkausthu, I cannot see the image attached. Can you fix the link? ...
written 8 weeks ago by bernatgel1.2k
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Answer: A: Tools for visualization of CNVs called by XHMM
... Hi @nkausthu, I've not used XHMM myself, but if you can load the data into R, you can plot the data using [karyoploteR](http://bioconductor.org/packages/karyoploteR/). I've created a small simulated results using the .xcnv as decribed in the [XHMM tutorial](https://atgu.mgh.harvard.edu/xhmm/tutor ...
written 8 weeks ago by bernatgel1.2k
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Answer: A: Getting a bash pipeline to output non-zero exit code when a step fails
... I like the explicit error management described [here][1], with a try, yell and die functions. As a bonus, you can modify die to do some additional logging of errors before actually dying and returning. It might be useful in addition to pipefail yell() { echo "$0: $*" >&2; } die() { y ...
written 11 weeks ago by bernatgel1.2k
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Comment: C: Tools for visualizing genome
... Aritra, We would need more information to help you. Do you have the positions of the STRs or you need to compute them? As I understand your questio, you don't actually need to visualize the sequence, isn't it? If you have the positions of the STR's in a BED file or similar, you can use [karyoplot ...
written 5 months ago by bernatgel1.2k
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Comment: C: Creating chromosome karyotype plot with R and ggplot2
... Ok, I'll do that. thanks ...
written 6 months ago by bernatgel1.2k
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Tutorial: Creating a karyotype plot with genes using karyoploteR
... Note: This post was an answer to [another Tutoria doing the same with ggplot](https://www.biostars.org/p/269857/). Moved here as suggested by others. I had to create whole genome plots with data on them more than than a few times, and it's not easy to get it right! So I finally decided to create a ...
genome R tutorial visualization karyoploter written 6 months ago by bernatgel1.2k

Latest awards to bernatgel

Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Teacher 11 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
Guru 6 months ago, received more than 100 upvotes.
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 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 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
Librarian 8 months ago, created a post with more than 10 bookmarks. For karyoploteR: uncircle your genomes
Scholar 10 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Prophet 10 months ago, created a post with more than 20 followers. For karyoploteR: uncircle your genomes
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Teacher 10 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 11 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 11 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 11 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 11 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 11 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 11 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: Permutation test with gene size and GC contents
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
Teacher 15 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

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