User: ngs06

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ngs0620
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Posts by ngs06

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Comment: C: how does "maxgap" in ChIPpeakAnno working?
... Thanks Julie, for your clarification:) ...
written 7 months ago by ngs0620
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Comment: C: how does "maxgap" in ChIPpeakAnno working?
... Yes, coming back to my main question. If "both" is considering overlapping features with maxgap:5000 then why does it reported the gene Cpa6 as its "overlapping" with distance of 72153 (which is > 5000 bp) Example here: ``` seqnames start end width strand peakNames peak feature star ...
written 7 months ago by ngs0620
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Comment: C: how does "maxgap" in ChIPpeakAnno working?
... Thanks for your reply Ou! But i am using "both" option not the "nearestLocation" . And according to the manual maxgap should be considered for this parameter right? ```"both" will output all the nearest features, in addition, will output any features that overlap the peak that is not the nearest fea ...
written 7 months ago by ngs0620
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how does "maxgap" in ChIPpeakAnno working?
... Hi, I tried to annotate my chipseq peak called regions with ChIPpeakAnno package using the following command. If i understand correctly : output=both, annotates to the nearest features (upstream and downstream) as well as the features overlapping within given maxgap (i.e 5000 bp ) distance. ``` fi ...
chippeakanno written 8 months ago by ngs0620
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Comment: C: Problems installing RBGL in R
... It worked and error is solved. Thank you very much! ...
written 11 months ago by ngs0620
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Problems installing RBGL in R
... Hello, I have updated my R software to 3.5.1. I am trying to install 'RBGL' package and had problems installing it. Previously I was using R.3.4.4 and had no problems with 'RBGL ' installation Can anyone help me in pointing out, what the error message corresponds to? And here is gcc version deta ...
rbgl r package problem written 11 months ago by ngs0620 • updated 11 months ago by Martin Morgan ♦♦ 23k
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Comment: C: ChipSeq binning and normalization
... Thanks Aaron for quick response! I will go through the package .. ...
written 4.1 years ago by ngs0620
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ChipSeq binning and normalization
... Hi, In most of the chipseq papers, inorder to visualize the intensity signals the data is represented in the form of normalized counts. One such is this paper http://www.nature.com/nature/journal/v488/n7409/full/nature11243.html, in the supplementary methods they described the procedure as "To gen ...
chipseq bioconductor written 4.1 years ago by ngs0620 • updated 4.1 years ago by Aaron Lun25k

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Popular Question 11 months ago, created a question with more than 1,000 views. For ChipSeq binning and normalization

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