User: s1437643

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s14376430
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Posts by s1437643

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Removing GC content bias and trended bias from ChIP-seq data
... Note: I originally posted this on Biostars, but was suggested to post here. I am doing DB analysis of ChIP-seq data using the csaw package. It seems I have a small trended bias and possible GC content bias in my data. Below are MA plots showing signal in the merged peaks using CPM normalisation (LH ...
normalization edger cqn chip-seq csaw written 3.0 years ago by s14376430 • updated 3.0 years ago by Aaron Lun25k
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How to retrieve ranges within 1000bp of each range in an IRanges object?
... I have an IRanges object which contains regions of interest and read counts for a given sample in the metadata column. I would like to iterate through each of the regions and get the counts for regions which are within 1,000 bp of the current region. I have tried the following but It is too slow and ...
iranges written 3.7 years ago by s14376430 • updated 3.7 years ago by Michael Lawrence11k
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What is the difference between 'sigma' and 'sig2' in CQN package?
... I'm following along with the vignette for CQN and I encountered a message which I don't understand. When using the cqn function the SQN package it calls states that it is using 'sigma' instead of 'sig2'. I'm not sure what this means, or what affect this has on the results of the cqn package, or its ...
cqn sqn written 3.8 years ago by s14376430

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