User: 94133

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941330
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Posts by 94133

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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... Great, thanks for your quick reply! ...
written 21 days ago by 941330
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... Thanks! Is there a way to keep res as "GRanges" object?   ...
written 21 days ago by 941330
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... Thanks for your reply! I tried that but get: Error in as.vector(x) : no method for coercing this S4 class to a vector Suggestions? I made workaround with dplyr, but have to convert from class "GRanges" to "data.frame" to do that.       ...
written 21 days ago by 941330
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ChIP peak annotation: how to get all genes that overlap each peak?
... How do I get all genes that overlap a peak as a comma separated column within a single row for the peak? I tried ChIPseeker: annotatePeak(peaks, level = "gene",                           addFlankGeneInfo = FALSE,                          assignGenomicAnnotation = TRUE,                          TxD ...
chippeakanno chipseeker chip-seq written 22 days ago by 941330
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Comment: C: CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of
... Do you have a suggested workflow for aligning to combined genomes? I agree with the points that you raised here, thanks for your input! The primary advantage of spike-in normalization is to draw empirical quantitative normalization between control and treated samples, especially in cases where ther ...
written 11 weeks ago by 941330
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Comment: C: CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of
... Thank you for your help! Wouldn't aligning to a combined human/mouse reference (presumably by changing chrom names, i.e. mchr1 v hchr1) suffer from the same putative double mapping issue? Alternatively, one could throw out reads that map to both genomes, but this seems like a very bad idea because ...
written 11 weeks ago by 941330
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CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of 'se.out' and 'object' are not identical
... I am trying to normalize ChIP-seq data using an exogenous spike in control with csaw and get the following error:  >filtered.data <- normOffsets(filtered.data.spike, se.out=filtered.data) Error in .local(object, ...) :    library sizes of 'se.out' and 'object' are not identical library(csaw ...
software error R bioconductor chip-seq csaw written 11 weeks ago by 941330 • updated 11 weeks ago by Aaron Lun20k

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