User: alex.gos90

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alex.gos9010
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11 months, 1 week ago
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Posts by alex.gos90

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Gviz single side margin for plotTracks
... Hi Robert, this would be really nice! I do not know how much sense it makes, but maybe you could allow both versions to be used. So providing either two or four values, these could be interpreted differentially.    Best Alex  ...
written 11 months ago by alex.gos9010
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Comment: C: Gviz single side margin for plotTracks
... Thanks Robert for pointing this out.  Now I actually played around a bit more (before was taking too long) and figured out you can basically only extend margin in horizontal (equally left/right) and vertical (equally top/bottom) direction.  This sounds definitely better than my first assumption wit ...
written 11 months ago by alex.gos9010
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Comment: C: DESeq2 for Cut&Run and differential enrichment testing
... I should add that I have used it for ATACseq data, but I do not know how it performs with broad ChIPseq.  ...
written 11 months ago by alex.gos9010
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Answer: A: DESeq2 for Cut&Run and differential enrichment testing
... Hi, I was recently very happy to find RUVSeq (https://bioconductor.org/packages/release/bioc/html/RUVSeq.html) for normalisation prior differential analysis. They have a method specifically developed for spike-in normalisation (RUVg), and provide further advice how to proceed with DEseq2. Maybe th ...
written 11 months ago by alex.gos9010
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How to left or right align titles in Gviz tracks?
... Hi fellow Gviz developers and users,    First of all thank you for providing the awesome Gviz package for plotting genomics data, it is really extensible and looks very nice with minimal tweaking.  Currently I am using Gviz for plotting some browser snapshots directly from bigwig files, which wor ...
gviz title grid text formatting written 11 months ago by alex.gos9010
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Gviz single side margin for plotTracks
... Hi Gviz developers,    I found the option to increase the margin around the plot area very helpful to include longer than usual titles, but when I tried in par(mar(c(bottom, left, top, right))-like manner to specify side specific margins it did not work as expected.  Somehow the margin was defined ...
gviz layout grid written 11 months ago by alex.gos9010 • updated 11 months ago by Robert Ivanek650
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large memory footprint with summarizeOverlaps method for BamViews
... Hello, I would like to point out, that when I use a BamViews object that was defined with a specific bamRanges with the summarizeOverlaps method, the whole Bam file is loaded into Memory, if I do not explicitly provide the param argument. Here is an example library(GenomicAlignments) tiny_bam &l ...
rsamtools genomicalignments summarizeoverlaps bamviews written 19 months ago by alex.gos9010 • updated 19 months ago by Martin Morgan ♦♦ 24k
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Comment: C: Gviz: Add label/title to GenomeAxisTrack
... Hi Robert, thank you very much, that was much easier than expected.  Best, Alex ...
written 21 months ago by alex.gos9010
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Gviz: Add label/title to GenomeAxisTrack
... Dear Gviz Developers, thank you for creating such a wonderful package.   I am working with the genome 'ce10', for which there is no cytoband data available at UCSC and therefore no IdeogramTrack is possible. Now I would like to know, whether it is possible to place a title or label to the left o ...
celegans gviz written 21 months ago by alex.gos9010 • updated 21 months ago by Robert Ivanek650
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Comment: C: Remote rejected after resetting to previous commit
... Hi, Thank you for your answer! As there were no issues with the code in it's current state I will ignore those duplicate commits,  but definitely will pay more attention when updating the repo.    ...
written 21 months ago by alex.gos9010

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