User: Ou, Jianhong

gravatar for Ou, Jianhong
Ou, Jianhong1.1k
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j**********@duke.edu

Posts by Ou, Jianhong

<prev • 184 results • page 1 of 19 • next >
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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 9 days ago by Ou, Jianhong1.1k
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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 7 weeks ago by Ou, Jianhong1.1k
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Comment: C: ATACseqQC installation fails at shiny step
... try: install.packages(c("Rcpp", "httpuv", "shiny")) ...
written 7 weeks ago by Ou, Jianhong1.1k
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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 9 weeks ago by Ou, Jianhong1.1k
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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 9 weeks ago by Ou, Jianhong1.1k
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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 9 weeks ago by Ou, Jianhong1.1k
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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 9 weeks ago by Ou, Jianhong1.1k
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Comment: C: trackViewer, the interactive version, can't view negative values in bigWig
... Please have a try the newest docker. It should be OK to visualize the bw files with both positive and negative values. ...
written 11 weeks ago by Ou, Jianhong1.1k
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Comment: C: How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
... You may want to try : ``` out <- binOverFeatureCpG.gr, annotationData=mes.gr, select = "nearest", PeakLocForDistance="middle", featureSite="bothEnd", radius=5000, nbins=100, FUN=length, errFun=sd, ylab="co ...
written 11 weeks ago by Ou, Jianhong1.1k
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Comment: C: factorFootprints, bindingSites and Profile.segmentation
... The bindingSites option can accept an GRanges object with binding score by any tools that can predict the binding sites. Please note that the "score" must be a column in the metadata. That means you can use matchPWM or fimo to predict the binding sites. The output of factorFootprints is very simil ...
written 11 weeks ago by Ou, Jianhong1.1k

Latest awards to Ou, Jianhong

Popular Question 10 months ago, created a question with more than 1,000 views. For installing Rgraphviz under CentOS 5.6
Scholar 10 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
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
Popular Question 15 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
Scholar 2.3 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 2.3 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Popular Question 2.3 years ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
Scholar 2.3 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 2.6 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Scholar 3.6 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 3.6 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 3.6 years ago, created 100 posts.
Scholar 4.0 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 4.9 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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