User: afli

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afli0
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Posts by afli

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Downstream proportions are not identical in vennpie and upsetplot results
... Thanks my friend, I see the post and UpSetR is recommended in the reply, I do not quite understand it why proportional Venn diagrams with 3 or more sets are not always possible, because UpSetR can easily handle six sets. Maybe I should think your advice further. ...
written 6 days ago by afli0
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Comment: C: Downstream proportions are not identical in vennpie and upsetplot results
... Yes, I used the example in your tutorial, and the same issue occur. My command lines are as follows: library(ChIPseeker) files <- getSampleFiles() peak <- readPeakFile(files[[4]]) require(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene peakAnno <- annot ...
written 6 days ago by afli0
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Downstream proportions are not identical in vennpie and upsetplot results
... ![enter image description here][1] [1]: https://de.cyverse.org/dl/d/0C23D88E-322F-479A-AF7B-E39589A0E75E/upsetplot.JPG Hi, I find that the peaks in downstream region is zero in upsetplot, but it take up some part in ven plot. Where is this difference come from? Thank you! ...
upsetplot chipseeker written 8 days ago by afli0 • updated 7 days ago by dariober9.3k
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Comment: C: How to get the all the overlap information of a peak in ChIPseeker
... Thank you my friend, and I found another answer below. ...
written 9 days ago by afli0
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Comment: C: How to get the all the overlap information of a peak in ChIPseeker
... Thank you I got it! features = attributes(peakAnno) head(features['detailGenomicAnnotation'][[1]]) the link is: https://github.com/GuangchuangYu/ChIPseeker/issues/43 ...
written 9 days ago by afli0
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How to get the all the overlap information of a peak in ChIPseeker
... Hi guys, I think there must be all the annotation information of one peak in ChIPseeker analysis, for example, a peak could overlap with an exon or an intron. But when I look into the annotation file using as.GRanges method, I could only see one feature corresponding to one peak. I use this command ...
detail information of peak chipseeker written 9 days ago by afli0
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Comment: C: ATAC-seq peak calling with MACS
... Hi, ZheFrench, the read position should be shifted +4 and -5 bp in the BAM file before macs2 callpeak? Thank you! ...
written 11 days ago by afli0

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