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Comment: Multifactorial Design for DESEQ2 by ATpoint ★ 2.4k

There is a section in the vignette that covers interactions and (depending on use case) how one can do a full factorial design to make inte…

Answer: Multifactorial Design for DESEQ2 by Michael Love 39k

For questions about the experimental design, I recommend to consult with a local statistician. I have to reserve my time on the support sit…

Answer: Merging samples from different sequencing runs by Michael Love 39k

We often use RUV in the lab, and you would include the factors of unwanted variation in the design formula. See the workflow for example co…

Comment: Duplicate row.names when building SummarizedExperiment with make_se in DEP by Simran • 0

did you get your answer? I've been using DEP several times but the error only shows up now for some reason?

Comment: Does DiffBind make consensus peaks sets for samples from a given condition (e.g. by tahir.msajid • 0

Got it. Thank you Rory.

Votes

A: Deseq2: RNA-seq and Negative binomial distribution

A: DESeq2 and shrinkage of log2 fold changes

Filtering low variance genes for WGCNA

Calculation of module membership in WGCNA

A: converting ensembl transcript ID to ensemble gene: problem & missing values

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