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5.9 years ago
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I have a serious of time-queued chip-seq data and have called peaks.Is there any software that can help me to find out which peaks are dynamic?
Usually, the tool that you use to call peaks will additionally provide functionality for finding differential binding between peaks in different samples. Which 'tool' have you used?
I use MACS/MACS2 to call the peaks.And it do have function to find different peaks in two samples.But I need to find the different peaks in multiple samples(three?four?or more?).This tool seems to can not support this...
You're right, these tools focus on comparing one condition versus another. Were you looking for something like ANOVA between all of your condition?
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows allows for this. It comes from a reputable pair of authors.