User: linuxborg2

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linuxborg20
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Posts by linuxborg2

<prev • 5 results • page 1 of 1 • next >
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permTest plot Evobs bar moves and it should not
... I got permTest working thanks to my questions about how to use permTest here https://support.bioconductor.org/p/107392/ but now I need to understand why my plotted Evobs bar moves.   red is alpha=0.05 (tail), the significance limit green is Evobs, average distance of QKI binding sites to intron-ex ...
regioner permtest written 16 months ago by linuxborg20
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Comment: C: permutation test on one set of data to get p-value of highest peaks. permTest?
... I got the standard randomizeRegions and meanDistance to work, but I am not sure that my custom genome (I want hg38 not the default hg19) and mask variables were put into randomizeRegions because I was unable to put the genome and mask variables inside of randomizeRegions and instead had to put them ...
written 17 months ago by linuxborg20
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Comment: C: permutation test on one set of data to get p-value of highest peaks. permTest?
... Thank you your comment helped me make a lot of progress.  I still have questions about evaluate.function and randomize.function.   Can I do this then trim the result in AWK to only be peaks closer than 300 bps to an intron-exon boundary? evaluate.function=meanDistance(test.bed, exonintronjunction ...
written 17 months ago by linuxborg20
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permutation test on one set of data to get p-value of highest peaks. permTest? How?
... How do I do a permutation test on one bed file of data to get the p-value of the highest peaks of distance frequency?  Is permTest what I want? (https://www.rdocumentation.org/packages/regioneR/versions/1.4.0/topics/permTest)   I am measuring QKI binding sites at exon-intron junctions.  Right now ...
regioner permtest written 17 months ago by linuxborg20
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I need to measure distance of PAR-CLIP data to RNA regions
... Please help me find the right Bioconductor packages for my Masters thesis. https://www.bioconductor.org/packages/release/BiocViews.html#___Software   SF1 and QKI are involved in splicing regulation, alternative splicing, and circRNA biogenesis.  QKI is a tumor suppressor and inhibits tumorigenici ...
gff3 bedtools bed files parclip written 19 months ago by linuxborg20

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