User: Ou, Jianhong

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Ou, Jianhong1000
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Posts by Ou, Jianhong

<prev • 122 results • page 1 of 13 • next >
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Answer: A: How to change seqlevels in a GRanges object
... Did you tried seqlevelsStyle? ...
written 3 months ago by Ou, Jianhong1000
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Answer: A: Annotation Database for ChIPpeakAnno
... Thank you to use ChIPpeakAnno package to annotate your data.  In current release version of ChIPpeakAnno, any annotation data in GRanges format will be acceptable. In your case, you can download most recently annotations via HUGO or Ensembl (in same assembly). You can also follow the vignettes in C ...
written 3 months ago by Ou, Jianhong1000
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Answer: A: trackviewer lolliplot pie.stack
... Thank you for select trackViewer to plot your data. For pie.stack layout, it is designed to aligned by row for each stack.factor. I know if there are many factors, it will be better to line up on top of each other. But in the released version, it is impossible. I will add some arguments to do this ...
written 4 months ago by Ou, Jianhong1000
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Answer: A: mm10 phastCons data for use with ATACseqQC
... Here is my old code to generate phastCons60w.UCSC.mm10. It may not work because it is not in GScores format. But maybe you can have a try.   system("wget http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/mm10.60way.phastCons.bw") library(BSgenome.Mmusculus.UCSC.mm10) library(GenomeIn ...
written 4 months ago by Ou, Jianhong1000
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Answer: A: RNAseq read coverage plot: What tool?
... Givz or trackViewer? ...
written 5 months ago by Ou, Jianhong1000
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Comment: C: ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is d
... Hi, I will show some sample codes to answer your question. Hope this can help you to understand what happened for the Venn-diagram. For question 1: There is a column in the metadata of each element in peaklist, called peakNames, which is a CharacterList. The CharacterList is a list of the contrib ...
written 6 months ago by Ou, Jianhong1000
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Answer: A: ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is d
... Hi, This question has been asked many times. Please refer the answer in https://support.bioconductor.org/p/62739/#62976 You can have a try to turn on the argument connectedPeaks="keepAll" to see how the numbers change. Basically, the merged peaks may be different from the original peaks because t ...
written 6 months ago by Ou, Jianhong1000
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Answer: A: ChIPpeakAnno, MACS format annotation
... Hi, Thanks for selecting ChIPpeakAnno as your annotation tool. First question, that is a warning. I am consider to change it to a message. That message tells you the function could not find peak name or there are duplicated peak names. And the toGRanges function will automatically give a name for ...
written 6 months ago by Ou, Jianhong1000
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Comment: C: Error in GRanges: could not find symbol "recursive" in environment of the generi
... yes reinstall biocLite(c("BiocGenerics", "XVector", "S4Vectors", "IRanges", "GenomicRanges"), type="source") will help. ...
written 7 months ago by Ou, Jianhong1000
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Comment: C: question about summrizeOverlaps
... Good to know. I misunderstand the meaning of GRangesList in this function. Thank you. ...
written 7 months ago by Ou, Jianhong1000

Latest awards to Ou, Jianhong

Scholar 3 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
Scholar 6 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 19 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
Centurion 19 months ago, created 100 posts.
Scholar 23 months ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 2.9 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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