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User: Ou, Jianhong

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Ou, Jianhong1.1k
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Posts by Ou, Jianhong

<prev • 156 results • page 1 of 16 • next >
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Comment: C: how does "maxgap" in ChIPpeakAnno working?
... "both" means it will include all the results of nearestLocation and overlapping. I understand that this is a little confusion. ...
written 4 days ago by Ou, Jianhong1.1k
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Answer: A: The meaning of results produced by the bamQC function implemented in the ATACseq
... Hi Gary, (1) The meaning of $totalQNAMEs Total number of reads (single, paired) (3) The meaning of $MAPQ. Is it mapping quality? Yes. It is the count of each mapping quality value. (4) How does ATACseqQC define the low mapping quality in $notPassingQualityControlsRate ATACseqQC did not define the ...
written 4 days ago by Ou, Jianhong1.1k
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Comment: C: how does "maxgap" in ChIPpeakAnno working?
... NearestLocation will ignore the maxgap parameter. If you want all annotation within 5K of gene, you can filter it after annotation. See https://support.bioconductor.org/p/60971/ Jianhong. ...
written 4 days ago by Ou, Jianhong1.1k
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Answer: A: Methylation data visualization using methyAnalysis with minfi
... You can have a try with: asy <- assays(gmset) asy[["exprs"]] <- getBeta(gmset) names(asy) <- c("methylated", "unmethylated", "exprs") yyy <- MethyGenoSet(rowRanges=rowRanges(gmset), assays=asy, pData=colData(gmset))   If you just want to see the signals, maybe you want to have a try w ...
written 10 weeks ago by Ou, Jianhong1.1k
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Comment: C: error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnal
... I just tried the development version. And I found that this issue is already resolved in the development version. So I closed the question by myself. Thank you. ...
written 4 months ago by Ou, Jianhong1.1k
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Comment: C: error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnal
... Hello Ou, Jianhong! We believe that this post does not fit the main topic of this site. This is fixed in development version For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why ...
written 4 months ago by Ou, Jianhong1.1k
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(Closed) error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnalyzeR
... Hi Kristoffer Vitting-Seerup, I am trying to use IsoformSwitchAnalyzeR to analyze my RNAseq data. When I trying to run analyzeAlternativeSplicing, I got error: Error in `[.data.frame`(localExonSkippingIndex, 1) : undefined columns selected Is there any thing I missed? Here is my code: lib ...
isoformswitchanalyzer written 4 months ago by Ou, Jianhong1.1k
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Comment: C: ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... try: ChIP_peaks_annoTSS_cond <- condenseMatrixByColnames(as.matrix(as.data.frame(unname(ChIP_peaks_annoTSS))), "peak") ...
written 5 months ago by Ou, Jianhong1.1k
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Comment: C: ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... This will find the peaks overlap with the TSS because we set the maxgap=-1 and FeatureLocForDistance="TSS".  However, maybe this is not the answer of your biological question. Maybe you are asking to find the annotation for promoter region? If that is the case, please try to use set output="overlap ...
written 5 months ago by Ou, Jianhong1.1k
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Answer: A: ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... Did you tried to set output = "upstream"? ...
written 5 months ago by Ou, Jianhong1.1k

Latest awards to Ou, Jianhong

Popular Question 5 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Popular Question 7 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 20 months ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 20 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Popular Question 20 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 20 months ago, created an answer that has been accepted. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
Scholar 20 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
Scholar 23 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 3.0 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 3.0 years 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 3.0 years ago, created 100 posts.
Scholar 3.3 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 4.3 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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