User: bernatgel

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bernatgel950
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Barcelona, Spain
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@bernatgel
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Posts by bernatgel

<prev • 54 results • page 1 of 6 • next >
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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 19 hours ago by bernatgel950
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Comment: C: Creating chromosome karyotype plot with R and ggplot2
... Ok, I'll do that. thanks ...
written 1 day ago by bernatgel950
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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 1 day ago by bernatgel950
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Answer: A: Creating chromosome karyotype plot with R and ggplot2
... Hi steve, Thanks for the tutorial. I had to create plots like this more than than a few times, and it's not easy to get it right! So I finally decided to create a package to make my life easier. I'd be happy if you to give it a try :) It's called [karyoploteR](https://academic.oup.com/bioinformati ...
written 1 day ago by bernatgel950
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Answer: A: How to plot B-allele frequency and Log R ratio using R
... To plot data along the genome you can use [karyoploteR](http://bioconductor.org/packages/karyoploteR). It's in Bioconductor (so you can install it with `biocLite(karyoploteR)` and can plot almost anything on almost any genome. There's a [tutorial and examples page](https://bernatgel.github.io/kary ...
written 2 days ago by bernatgel950
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Answer: A: Drawing yeast chromosome ideograms with data
... Hi Marco, If you are still interested in this, I would suggest you to try [karyoploteR](https://academic.oup.com/bioinformatics/article/33/19/3088/3857734), it's an [R/Bioconductor package](http://bioconductor.org/packages/karyoploteR) to plot genomes (and parts of them) with data. And most import ...
written 2 days ago by bernatgel950
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Answer: A: Drawing Chromosome Ideograms With Data
... This is an old question, but since it's referenced multiple times as a list of tools to create karyotype plots, I'll add karyoploteR too. karyoploteR is an [R/Bioconductor package](http://bioconductor.org/packages/karyoploteR) to create plots of genomes (or parts of them) and add data positioned al ...
written 3 days ago by bernatgel950
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Comment: C: How to name the genome in karyoploteR ?
... Have you loaded the BSgenome before calling karyoploteR? You can either pass karyoploteR the name of the genome (in this case "TAIR9") and it will try to find and load the genome library(karyoploteR) kp <- karyoploteR::plotKaryotype(genome = "TAIR9") (in this case it will give you some ...
written 3 days ago by bernatgel950
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Answer: A: How to name the genome in karyoploteR ?
... Hi @kirannbishwa01, It should work as you are doing but it for some reason it does not work with this BSgenome. karyoploteR ultimately relies on the function `getBSgenome` from `BSgenome` to load the necessary BSgenomes on the fly. As an example I tried downloading and installing `"BSgenome.Vvinif ...
written 19 days ago by bernatgel950
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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 10 weeks ago by bernatgel950

Latest awards to bernatgel

Guru 1 day ago, received more than 100 upvotes.
Teacher 2 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
Teacher 24 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
Librarian 10 weeks ago, created a post with more than 10 bookmarks. For karyoploteR: uncircle your genomes
Scholar 4 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Prophet 4 months ago, created a post with more than 20 followers. For karyoploteR: uncircle your genomes
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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
Appreciated 5 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 5 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 5 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 5 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 5 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 5 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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Scholar 8 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
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 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
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