User: Ou, Jianhong

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Ou, Jianhong1.1k
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Posts by Ou, Jianhong

<prev • 146 results • page 1 of 15 • next >
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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 22 days 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 22 days 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 22 days 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 22 days ago by Ou, Jianhong1.1k
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Answer: A: Compare the DNA footprinting between different samples when using ATACseqQC
... Hi Aimin, Now, in the next development version, you can control ylim. I add this possibility today. You can try it by library(devtools); install_github("jianhong/ATACseqQC") The dot red lines is the fragmentation fit line of the signals. If you want to compare footprinting between different samp ...
written 23 days ago by Ou, Jianhong1.1k
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Comment: C: Error creating pool for permutation test (PeakPermTest)
... Hi Gema, Thank you for using ChIPpeakAnno. Could you sent me the sessionInfo? I can not repeat your error on my computer. Or you can try to update all your package into nearest version. Jianhong.   ...
written 26 days ago by Ou, Jianhong1.1k
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... try to add scores for the binding sites like this  which$score <- rep(1, length(which)) ...
written 4 weeks ago by Ou, Jianhong1.1k
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Answer: A: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... Hi Aimin, Thank you for trying ATACseqQC to plot the TF footprints. You can have a try following code: which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 20000, by=1000), width = 10)) seqinfo(which) <- seqinfo(Hsapiens) factorFootprints(bamfile, pfm=CTCF[[1]], ...
written 4 weeks ago by Ou, Jianhong1.1k
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Comment: C: How to understand Summary.xls in output of CRISPRseek
... Thank you Julie for the correction. Jianhong. From: "Julie Zhu [bioc]" <noreply@bioconductor.org> Reply-To: "reply+e0a20045+code@bioconductor.org" <reply+e0a20045+code@bioconductor.org> Date: Friday, June 8, 2018 at 10:05 AM To: "Jianhong Ou, Ph.D." <jianhong.ou@duke.edu> Subject ...
written 9 weeks ago by Ou, Jianhong1.1k
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How to understand Summary.xls in output of CRISPRseek
... Hi Julie, I want to double check that I correctly understand each column of summary.xls in output of CRISPRseek. Thank you. names : name of gRNA   forViewInUCSC : coordinates   extendedSequence : extended sequence of gRNA   gRNAefficacy : gRNA efficacy. The higher the better. see [https://ww ...
crisprseek written 9 weeks ago by Ou, Jianhong1.1k • updated 9 weeks ago by Julie Zhu3.8k

Latest awards to Ou, Jianhong

Scholar 13 months ago, created an answer that has been accepted. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
Popular Question 13 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 13 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 13 months ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
Scholar 13 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 16 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 2.4 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 2.4 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 2.4 years ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 3.8 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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