User: bernatgel

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bernatgel1.2k
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@bernatgel
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Posts by bernatgel

<prev • 64 results • page 1 of 7 • next >
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Comment: C: How to determine the surface markers in a gene list
... I would probably annotate them with Gene Ontology, with the "Cellular Compartment" part, and then look for membrane associated terms. ...
written 24 days ago by bernatgel1.2k
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Answer: A: plot genome using RCircos
... You can use [karyoploteR](https://github.com/bernatgel/karyoploteR) for that. It will draw the genome as lines instead of a circle, but it can work with any genome as long as you give it the chromosome names and lengths. It is not restricted to any species or any data provider such as UCSC or Ensemb ...
written 5 weeks ago by bernatgel1.2k
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Comment: C: A weird variant call from VarScan2 mpileup2snp
... My first option would be to visually inspect the BAM with IGV or similar and see if I can make sense of the numbers. ...
written 8 weeks ago by bernatgel1.2k
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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 9 weeks 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 9 weeks 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 3 months 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 4 months 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 4 months 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 4 months 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 4 months ago by bernatgel1.2k

Latest awards to bernatgel

Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Teacher 4 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
Guru 8 months ago, received more than 100 upvotes.
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
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
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
Librarian 10 months ago, created a post with more than 10 bookmarks. For karyoploteR: uncircle your genomes
Scholar 12 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Prophet 12 months ago, created a post with more than 20 followers. For karyoploteR: uncircle your genomes
Voter 12 months ago, voted more than 100 times.
Teacher 12 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 13 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 13 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
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 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
Appreciated 13 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
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 16 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 16 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 16 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 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

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