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cummeRbund Script analysis RNAseq cuffdiff

updated 9.9 years ago by andrew.j.skelton73 ▴ 370 • written 9.9 years ago by mfahim • 0

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Comment: Can't post a question? by DavideSant • 0

Thank you, this was super useful!

Comment: Error in retrieving clinical data by silickas • 0

Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…

Comment: deseq2 lfc shrinkage with few DEGs by Robert • 0

I'm dealing with a similar situation. I assume the coefficients related to batch effect would need to be included in idx also, is this corr…

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…

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