User: Ou, Jianhong

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Ou, Jianhong1.2k
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Posts by Ou, Jianhong

<prev • 187 results • page 1 of 19 • next >
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Comment: C: trackViewer: how to make lolliplots for methylation data
... Hi Patricia, If there are pins everywhere, you may want to try [dandelion plot](https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html#dandelion_plot). If there are multiple CpGs in one region, split it for each CpGs. Currently, lolliplot only support the pl ...
written 25 days ago by Ou, Jianhong1.2k
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Comment: C: trackViewer: how to make lolliplots for methylation data
... What kind of file do you have? Whatever files can be imported into GRanges is OK for trackViewer to do lolliplot. If you want to show differences in two conditions, you can show it one by one or show it in caterpillar layout. Because you may want to fix the methylation positions, you can try to set ...
written 4 weeks ago by Ou, Jianhong1.2k
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Answer: A: Can I use trackViewer to generate methylation lolliops with my own gene models a
... Hi John, You can always generate a TxDb object by functions makeTxDbFromGFF from a local gff file, or makeTxDbFromUCSC, makeTxDbFromBiomart, and makeTxDbFromEnsembl, from online resources in GenomicFeatures package. For trackViewer to plot lolliplot, you can just input a GRanges object as featur ...
written 6 weeks ago by Ou, Jianhong1.2k
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Answer: A: Error in running ATACseqQC
... Hi Fei, As Haibo suggested, to output figures, you'd better plot the figure to a device and close it after plot. length(names(obj)) == length(obj) is not TRUE means the length of name of gal1 is not identical to the length of gal. Please double check the names of gal1 to make sure that there i ...
written 7 weeks ago by Ou, Jianhong1.2k
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Comment: C: ATACseqQC installation fails at shiny step
... install.packages(c("Rcpp", "httpuv", "shiny"), repos="https://cloud.r-project.org") ...
written 3 months ago by Ou, Jianhong1.2k
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Comment: C: ATACseqQC installation fails at shiny step
... try: install.packages(c("Rcpp", "httpuv", "shiny")) ...
written 3 months ago by Ou, Jianhong1.2k
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Comment: C: How to change the size of yaxis in motifstack
... In current version, motifStack can not handle ylim. I want to fix the ylim when ic.scale is used. In your specific usage, you can have a try with plotMotifLogoA to plot the logos one by one like this (but I don't suggest you to do that): grid.newpage() vp <- viewport(x = .5, y=1.8, width = .9, he ...
written 3 months ago by Ou, Jianhong1.2k
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Comment: C: How to change the size of yaxis in motifstack
... something like this (see vignette and help files for more details): plot(motif, ic.scale=FALSE, ylab="probability") ...
written 3 months ago by Ou, Jianhong1.2k
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Comment: C: How to change the size of yaxis in motifstack
... If that is the case, I would suggest you to set ic.scale into FALSE. Please have a try and let me know if that meet your requirement. ...
written 3 months ago by Ou, Jianhong1.2k
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Comment: C: How to change the size of yaxis in motifstack
... Currently the yaxis is fixed by the max entropy of information. May I know why you want to change default yaxis? ...
written 3 months ago by Ou, Jianhong1.2k

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Scholar 2.5 years ago, created an answer that has been accepted. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
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Teacher 3.8 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?
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Scholar 4.1 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 5.1 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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