User: Nathan

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Nathan0
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Posts by Nathan

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Normalising Affymetrix Human Tiling 2.0R Set arrays for ChIP-chip
... Hi all, So I have a set of publicly available ChiP-chip data that uses the Affymetrix Human Tiling 2.0R Set. Which really means that each individual replicate has seven individual arrays associated with it. I am trying to use the Starr package from Bioconductor to analyse this data, and while I ...
bioconductor chip-chip tiling array written 2.2 years ago by Nathan0
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Comment: C: Specifying model in DESeq - differentiation experiment
... Thanks for the suggestion, but I'd already tried that approach and kept on coming up with the standard full rank model exception. I guess I'll more of a play with how best to separation conditions. ...
written 2.9 years ago by Nathan0
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Specifying model in DESeq - differentiation experiment
... Hi all, I am trying to figure out the best way to specify the following experiment in DESeq2. I have a differentiation expression consisting of five conditions, the original set of starting cells (Ctrl Day 0) which are then differentiated by adding X or by a slightly different route by adding X ...
experimental design deseq2 deseq rna-seq written 3.0 years ago by Nathan0 • updated 3.0 years ago by Carlo Yague4.6k
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Using Bayespeak for Paired-end reads
... Hi everyone,  I was wondering if anyone knew how well BayesPeak performs on paired-end ChIP-seq reads (MNase-treated) - or even if it can be ran on paired-end reads reliably?  I noticed in the original BayesPeak paper that its says that the model can be easily extended to accomodate paired-end rea ...
chip-seq peak-calling bayespeak written 5.3 years ago by Nathan0
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Access To Chains And Nets Which Don'T Appear To Be Available For The Ucsc
... Hi, So I would like to use build a vertebrate phylogenetic tree using only species which have high-quality high-coverage sequences. However, looking at the UCSC web browser and downloads it looks like I can only download pre-computed chains and nets (I really need maf and axt files) for specific s ...
sequence alignment ucsc written 6.7 years ago by Nathan0

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