User: aimin.at.work

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Posts by aimin.at.work

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Comment: C: Compare the DNA footprinting between different samples when using ATACseqQC
... Thank you, what does the fragmentation fit line of the signals indicates? Aimin   ...
written 8 weeks ago by aimin.at.work0
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Compare the DNA footprinting between different samples when using ATACseqQC
... I am using ATACseqQC to plot DNA footprinting.  I want to compare the DNA footprinting between different samples.  Would it be possible to get  DNA footprinting graphs with same scale to make them be comparable? For example, for CTCF, I got some from 0 to 0.2, other from 0 to 0.14, from 0 to 0.25, e ...
atacseqqc written 9 weeks ago by aimin.at.work0 • updated 8 weeks ago by Ou, Jianhong1.1k
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... OK, thank you very much. it works now. Aimin On Thu, Jul 12, 2018 at 5:23 PM, Julie Zhu [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Julie Zhu <https: support.bioconductor.org="" u="" 3596=""/> wrote Answ ...
written 10 weeks ago by aimin.at.work0
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... Yes, I tried, but I got the following error: bamfile <- system.file("extdata", "GL1.bam",package="ATACseqQC") which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 20000, by=1000), width = 10)) seqinfo(which) <- seqinfo(Hsapiens) which$score <- rep(1, length(which)) factor ...
written 10 weeks ago by aimin.at.work0
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... Thank you, Yes, I tried, but I got same error as before. Aimin > which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 20000, by=1000), width = 10)) > which GRanges object with 11 ranges and 0 metadata columns: seqnames ranges strand <rle> <ira ...
written 10 weeks ago by aimin.at.work0
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use factorFootprints function in ATACseqQC to get DNA footprinting for certain gene region
... I am using your ATACseqQC to generate DNA footprinting for certain gene region.   I noted that for the function of factorFootprints, there is an argument of “bindingSite” to define gene region, so I did something like the following:   which <- GRanges(seqnames = “chr1", ranges = IRanges(1000 ...
atacseqqc written 10 weeks ago by aimin.at.work0 • updated 10 weeks ago by Julie Zhu3.8k
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Answer: A: how overlap between peaks is calculated in diffbind
... Rory, Yes, after I sort the peaks using DiffBind:::pv.peaksort. It works perfectly. Thank you very much. Aimin ...
written 14 months ago by aimin.at.work0
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how overlap between peaks is calculated in diffbind
... I am using DiffBind to find the overlapped peaks. I used the following commands: mcf <- dba.peakset(mcf,peaks=peaks.v,peak.caller=peak.caller.v, sampID=sampID.v,tissue=tissue.v,                           factor=factor.v,condition=condition.v,replicate=replicate.v) dba.plotVenn(mcf,mask=c(17,1 ...
diffbind written 14 months ago by aimin.at.work0

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