User: jun.yu

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jun.yu0
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Posts by jun.yu

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Answer: A: ChIPpeakAnno to find peaks nearest to miRNA
... xyang2, There is a new function called annoPeaks() in ChIPpeakAnno now. annoPeaks (peaks, annoData, bindingType=c("nearestBiDirectionalPromoters", "startSite", "endSite", "fullRange"), bindingRegion=c(-5000, 5000), ignore.peak.strand=TRUE, ...
written 12 weeks ago by jun.yu0
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Answer: A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
... Yi-Fang, I think org.db is organism level annotation, with is not connected with any specific genome assembly or annotation. ...
written 12 weeks ago by jun.yu0
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Answer: A: ChIPpeakAnno
... The p-value is calculated by hypergeometric test to determine whether the peaks or features are overlapped significantly in the makeVennDiagram function. Hypergeometric test requires users to input an estimate of the total potential binding sites (peaks) for a given TF. To circumvent this requiremen ...
written 12 weeks ago by jun.yu0
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Answer: A: featureAlignedSignal() error: deparse(sig): object 'sig' not found.
... Alex, I ran your code with some of my test file. It ran successfully. The ChIPpeakAnno has been updated many times since your question. I hope the new version solved your problem.   > gr_center GRanges object with 51385 ranges and 2 metadata columns:                 seqnames           ranges st ...
written 12 weeks ago by jun.yu0

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