User: Ou, Jianhong

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Ou, Jianhong1.1k
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Posts by Ou, Jianhong

<prev • 162 results • page 1 of 17 • next >
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Comment: C: chippeakanno file reading error
... you have typo, change brg1bed to brg1.bed for more information please refer:https://cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf ...
written 27 days ago by Ou, Jianhong1.1k
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Answer: A: chippeakanno file reading error
... suppose your brg1.bed is in current working directory, please try to run: grbrg1 <- toGRanges("brg1.bed", format="BED", header=FALSE) ...
written 27 days ago by Ou, Jianhong1.1k
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Answer: A: how can I convert a sequence to number
... Is this a good way to show your sequence as a motif logo? It is not suggested. Whatever, you can try following code to plot your sequence. seq <- "MGLRYSIYIENPLSSPSSSYKSINDPLFHSQHRSQKNVSFITYGCRHCKTHLSSSFQIIS RDYRGRTGTAYLMNKVVNVVEGKVEQRRMLTGDYLVCDILCHWCKRNVGWKYLQSSNDDQ QYKEGKFILELKNI ...
written 28 days ago by Ou, Jianhong1.1k
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Comment: C: motifStack crashes for example from documentation
... Hi Zixi, Great to know you figure it out! Jianhong ...
written 5 weeks ago by Ou, Jianhong1.1k
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Comment: C: motifStack crashes for example from documentation
... Hi Zixi, Sorry for the late reply. I tried to repeat your error in centOS 6.10 (docker to centOS 6.6 is not working). However I can not repeat it. I think main issue may be caused by the library of libxml2-devel or curl-devel. You can have a try to reinstall the grImport by giving it correct libxml ...
written 6 weeks ago by Ou, Jianhong1.1k
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Comment: C: motifStack crashes for example from documentation
... Hi chenzixi, Thank you for confirm this segment fault agian. Could you try to re-install grImport from source like this: install.packages("grImport", type="source") and then re-run the code above. Before you run pic <- readPicture(paste0(tmp, ".xml")), could you please run sessionInfo() and s ...
written 7 weeks ago by Ou, Jianhong1.1k
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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 9 weeks 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 9 weeks 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 9 weeks 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 4 months ago by Ou, Jianhong1.1k

Latest awards to Ou, Jianhong

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
Popular Question 9 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 22 months ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 22 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Popular Question 22 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 22 months ago, created an answer that has been accepted. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
Scholar 22 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
Scholar 2.1 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 3.1 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 3.1 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 3.1 years ago, created 100 posts.
Scholar 3.5 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 4.4 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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