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updated 6.4 years ago by
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written 6.5 years ago by
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updated 7.3 years ago by
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written 7.3 years ago by
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Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
•
0
Thank you so much!! Yeah I had thought about this too, regarding the fact that DiffBind is a wrapper for counting peaks in this way in R di…
Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
by
aitor
•
0
Hi everyone.
I have a RIP-Seq analysis with 3 conditions and 3 assays (IP, IgG and Input for each of them). 4 replicates for each conditio…
Comment: Discrepancy between Excel TPP-TR reported values and the Melt Curve reported val
by
James W. MacDonald
68k
You will need to provide a self-contained example, or it is unlikely that anybody could debug any possible issue.
Answer: Limma - Complex 2-way multi-level contrast with paired samples
by
James W. MacDonald
68k
If you are fitting donor as a fixed effect you do not also need to fit as a random effect. The limma package fits a generalized least squar…
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
ATpoint
★
4.7k
Yes, perfectly valid. Analyzing counts from high-throughput experiments with DESeq2 (or edgeR, or limma) is standard. After all, what DiffB…
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