User: bernatgel
bernatgel • 770
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Posts by bernatgel
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... 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 14 days ago by
bernatgel • 770
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Answer:
A: RNA seq Newbie needing help
... Performing an experiment with 576 samples without at least a small pilot seems quite risky. At least to check that there are some changes and that you can find the what you would clearly expect.
I think something like a pilot with two tanks, 2 time points (0 and 7), 2/3 fish per tank and a single ...
written 21 days ago by
bernatgel • 770
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... You can find [an example](https://bernatgel.github.io/karyoploter_tutorial//Examples/GeneExpression/GeneExpression.html) that might be helpful in karyoploteR's [Examples and Tutorial](https://bernatgel.github.io/karyoploter_tutorial/) site. It has complete code to get to something very similar to wh ...
written 23 days ago by
bernatgel • 770
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... I have no direct experience with any of them, but there are a few tools available for that. Some of them talk about targeted sequencing but do not specify if they would work for amplicons or only for hybridization based data. Most of them are designed to work with germinal data, since they are aimed ...
written 4 weeks ago by
bernatgel • 770
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... Hi @ajaybioinfo,
In your code, when you create the custom genome, you have two starts and only one chromosome. This creates an invalid genome (with two chromosomes of the same name) and prevent kpPlotDensity from working.
This should work
library(karyoploteR)
custom.genome <- toGRange ...
written 4 weeks ago by
bernatgel • 770
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... Hi,
Are you using the development version (it needs the development version of Bioconductor). The rainfall plot is only available in the development version right now and will be in release with the next Bioconductor release ( ~ October 2017). To use it you should install Bioconductor devel (you ha ...
written 6 weeks ago by
bernatgel • 770
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... Hi @nattzy94,
Right now only two data panels are implemented: one above and one below the chromosome.
However all of them can be partitioned to plot more than one data "track" with the parameters r0 and r1 (you can find more information on the [Data Postioning tutorial](https://bernatgel.github. ...
written 7 weeks ago by
bernatgel • 770
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... Hi @ajaybioinfo,
I've replied to the email you sent me.
Here's the reply
If you want to add some tracks with density data in the format you have given, you will only need to load that data into R and plot it with kpPlotDensity.
Please follow these steps:
1 - Load all your data into R. You can ...
written 7 weeks ago by
bernatgel • 770
2
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217
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Answer:
A: Add a legend to circos plot
... As far a I know, there is no functionality in Circos to add labels to tracks. We usually use an external program (Inskscape or similar) to add the labels when preparing the figure to publish.
Another option would be to use a text track with the track names, and try to position them as if they were ...
written 9 weeks ago by
bernatgel • 770
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... I edited the original answer to include some code ...
written 9 weeks ago by
bernatgel • 770
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