User: k.panov

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k.panov0
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Posts by k.panov

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Comment: C: DiffBind question: How to extract read counts?
... Hi Rory, Just to clarify, the counts extracted by dba.peakset function, aren't normalized to the library size, aren't they? Regards Konstantin   ...
written 5 months ago by k.panov0
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Comment: C: DiffBind question: How to extract read counts?
... Thank you very much Rory, that what I need . Regarding peak names, I just was not sure if any peak names (e.g. Peak 1, Peak 2 and so for) were given in addition to coordinates. Regards Konstantin ...
written 5 months ago by k.panov0
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DiffBind question: How to extract read counts?
... Hi Rory, I wonder, if it is possible to extract counting data (after performing dba.count) from a resulting DBA object in csv format where consensus peak names are in the first column, peak positions  are in the second/third/forth colums (chromosome, start, end) and  normalized number of reads for ...
diffbind read counts extract data written 5 months ago by k.panov0 • updated 5 months ago by Rory Stark2.5k
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error in TCseq
... Hello, I have following error message when I run TCseq 3.6 package:  > tca <- DBanalysis(tca) Error in .compressDispersions(y, dispersion) : dispersions must be finite non-negative values In addition: Warning message: In estimateDisp.default(y = y$counts, design = design, group = group, ...
tcseq written 6 months ago by k.panov0
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Comment: C: "input object should be a named list" error in ChIPseeker
... Cool, it works now! Thank you very much. Could I suggest to add this into ChIPseeker manual? Best regards Konstantin ...
written 6 months ago by k.panov0
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"input object should be a named list" error in ChIPseeker
... Hello, I am analyzing two MACS2 bed files using ChIPseeker. Individual analysis is OK, but I'm getting an error message for simultaneous analysis of two files when using following ChIPSeeker functions: plotAnnoBar, plotDistToTSS and vennplot. All error messages are similar: Error in XXXX (peakAnnoL ...
chipseeker vennplot named list error plotannobar plotdisttotss written 6 months ago by k.panov0 • updated 6 months ago by Guangchuang Yu1.0k

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