User: Ou, Jianhong

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Ou, Jianhong1.1k
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Posts by Ou, Jianhong

<prev • 181 results • page 1 of 19 • next >
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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 days 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 3 days 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 4 days 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 6 days 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 16 days 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 16 days 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 16 days ago by Ou, Jianhong1.1k
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Comment: C: atacseqQC error while splittin the bamfile
... you can update to the development version. Or set flag=scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery=FALSE, isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE) for readBamFile in released version to overcome the issue of all(elementNROWS(gal) < 3) is not TRUE see h ...
written 18 days ago by Ou, Jianhong1.1k
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Comment: C: trackViewer, the interactive version, can't view negative values in bigWig
... I will work on this soon. Best! Your sincerely, Jianhong Ou On Jul 31, 2019, at 11:27 AM, liruiradiant [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote: Activity on a post you are following on support.bioconduct ...
written 22 days ago by Ou, Jianhong1.1k
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Answer: A: trackViewer, the interactive version, can't view negative values in bigWig
... Hi Ray, You can put all the negative value into dat2 slot and convert the scores to positive. Best! Your sincerely, Jianhong Ou On Jul 30, 2019, at 7:48 AM, liruiradiant [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> ...
written 22 days ago by Ou, Jianhong1.1k

Latest awards to Ou, Jianhong

Popular Question 8 months ago, created a question with more than 1,000 views. For installing Rgraphviz under CentOS 5.6
Scholar 8 months ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Popular Question 11 months ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
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 2.2 years ago, created an answer that has been accepted. For A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
Scholar 2.2 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 2.2 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Popular Question 2.2 years ago, created a question with more than 1,000 views. For howto plot a figure like UCSC genome browser by Gviz
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Annotation Database for ChIPpeakAnno
Scholar 2.2 years 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
Scholar 3.5 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno
Teacher 3.5 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 3.5 years ago, created 100 posts.
Scholar 3.8 years ago, created an answer that has been accepted. For A: org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
Scholar 4.8 years ago, created an answer that has been accepted. For A: Curious behaviour of ChIPpeakAnno

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