User: Ou, Jianhong

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Ou, Jianhong1.1k
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Posts by Ou, Jianhong

<prev • 152 results • page 1 of 16 • next >
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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 8 weeks 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 8 weeks 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 8 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by Ou, Jianhong1.1k
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... NO. after merging, you can create a GRanges object by the new dataset. ...
written 4 months ago by Ou, Jianhong1.1k
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... try this: res <- condenseMatrixByColnames(as.matrix(as.data.frame(peaks_anno)), "peak") ...
written 4 months ago by Ou, Jianhong1.1k
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... Did you tried ?condenseMatrixByColnames for example: library(ChIPpeakAnno) res <- condenseMatrixByColnames(as.matrix(peaks_anno), "peak")   ...
written 4 months ago by Ou, Jianhong1.1k
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Comment: C: Compare the DNA footprinting between different samples when using ATACseqQC
... The fit line indicates distal cut-site probability, proximal cut-site probability and the TF avoidance cut-site probability. The difference between  proximal cut-site probability and the TF avoidance cut-site probability indicates the avoidance of the TFs. And the difference between distal cut-site ...
written 4 months ago by Ou, Jianhong1.1k

Latest awards to Ou, Jianhong

Popular Question 11 weeks ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Popular Question 4 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 17 months ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 17 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Popular Question 17 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 17 months ago, created an answer that has been accepted. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
Scholar 17 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
Scholar 20 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 2.8 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 2.8 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 2.8 years ago, created 100 posts.
Scholar 3.1 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 4.1 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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