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DESeq2 Normalization Clustering replicate

updated 12 days ago by Michael Love 43k • written 2.7 years ago by Giorgio • 0

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DEseq2 replicate DESeq2 normalization

3.4 years ago michael.morash • 0

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DiffBind ATACseq replicate

updated 4.5 years ago by Rory Stark ★ 5.2k • written 4.5 years ago by CodeAway ▴ 70

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deseq2 rnaseq replicate differential expression

updated 7.1 years ago by jovel_juan ▴ 30 • written 8.8 years ago by kieranrcampbell ▴ 50

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edgeR replicate

updated 8.5 years ago by nancyjwahl7 • 0 • written 9.3 years ago by Sushant Pawar • 0

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Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k

Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…

Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k

You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel

Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k

You show how you modified the container, but not how you are running it, which is the critical part.

Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0

Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …

Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k

Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…

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Answer: How to combine two DESeq2 objects (dds) for analysis

How to combine two DESeq2 objects (dds) for analysis

How can I correctly use phyloseq with Docker?

A: DESeq2::sizeFactors() function does not output the sizeFactor table.

Comment: Filtering after DESeq

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