User: bernatgel

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bernatgel60
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Posts by bernatgel

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Circos Tile colors
... I have successfully used Circos to plot copy number data, but I have no experience with OmicsCircos and similars. If you can accept a "linear" plot instead of circular you could take a look to karyoploteR. First create the sample data (with just two samples) and a few alterations. library(karyop ...
written 9 weeks ago by bernatgel60
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Comment: C: Error running the function permTest
... Hmm... I think it might come from an unavailable genome, although the error message should be quite more clear.  Could you check if the genome is available with  installed.genomes() You should see "BSgenome.Hsapiens.UCSC.hg19.masked" in the output. If it's not installed, try installing it with ...
written 9 weeks ago by bernatgel60
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Answer: A: Error running the function permTest
... I just run the full example in and it run without errors for me.  If you take a closer look at the error message it produced you can see it said 1: In mclapply(c(1:ntimes), randomize_and_evaluate, ...) : all scheduled cores encountered errors in user code That means that all parallel jobs sent e ...
written 9 weeks ago by bernatgel60
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Answer: A: how to plot human genome chromosome Ideogram with each length by Gviz
... You can use karyoploteR for that. You can create the complete ideograms for many different genomes (even for custom ones) and plot data on it if you want. IMPORTANT: karyoploteR is only available in Bioconductor devel until next release (mid April 2017) To create a simple ideogram of the human gen ...
written 3 months ago by bernatgel60
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Answer: A: Conflicting results in 'overlapPermTest' function from regioneR package
... Hi Vinicius, The problem may be due to how the overlaps are counted. When a region in A overlaps multiple regions in B it can be counted as one or multiple overlaps. By default, the function numOverlaps in regioneR counts them as multiple overlaps while your code counts the overlap only once. Actua ...
written 5 months ago by bernatgel60
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Comment: C: Sample code doesn't seem to be working on fresh install of regioneR
... Hi rcavalca, Actually BSgenome.Hsapiens.UCSC.hg19.masked is not a dependency but a suggested package.  The idea is that you need at least the BSgenome for the organism you want to work with. If you want to use the mask (so no regions ends up in the centromere, for example) then you should use the " ...
written 14 months ago by bernatgel60
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Answer: A: width(GRanges) increases after randomizeRegions(..) in package RegioneR
... Hi Ludo, You are completely right. This was a bug in the randomizeRegions code. I've fixed it and commited the changes to the release branch (Bioconductor 3.2) and so the new version regioneR 1.2.1 should be available on Bioconductor tomorrow. In addition, if you are using an older version of reg ...
written 16 months ago by bernatgel60
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Answer: A: Retrieving Regions from hg38 of the same GC content and length with a list of el
... Hi  Dimitris, For your first question: Yes, by default randomizeRegions uses the default mask of the genome (in this case the hg38masked) and so it won't create any of the new random regions in the repetitive regions. You second question is a bit more tricky. Right now regioneR does not have the f ...
written 19 months ago by bernatgel60

Latest awards to bernatgel

Scholar 9 weeks ago, created an answer that has been accepted. For A: Retrieving Regions from hg38 of the same GC content and length with a list of el
Scholar 16 months ago, created an answer that has been accepted. For A: Retrieving Regions from hg38 of the same GC content and length with a list of el
Scholar 19 months ago, created an answer that has been accepted. For A: Retrieving Regions from hg38 of the same GC content and length with a list of el

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