Bioconductor DES

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552

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 9 weeks ago by James W. MacDonald 66k • written 9 weeks ago by Alexandre • 0

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180

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Des DESeq2

updated 11 weeks ago by hemantcnaik • 0 • written 11 weeks ago by Sahar • 0

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292

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DESeq2 DEs

3 months ago feather-W • 0

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552

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DESeq2 des

updated 19 months ago by Michael Love 42k • written 20 months ago by Devin • 0

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605

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DES DESIGN

updated 21 months ago by Michael Love 42k • written 21 months ago by mike • 0

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659

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DESeq2 DES

updated 3.5 years ago by Michael Love 42k • written 3.5 years ago by heikki.sarin ▴ 10

6 results • Page 1 of 1

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Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k

As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…

Answer: LRT test for different timepoints (one tissue types vs. many tissue types) by Michael Love 42k

No, this is a contrast of estimated coefficient (e.g. the Wald test).

Comment: Ranking the GSEA Results by Michael Love 42k

Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…

Comment: Ranking the GSEA Results by V_Vibes • 0

I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…

Comment: Ranking the GSEA Results by V_Vibes • 0

The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…

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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)

ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features

Comment: How to get the DMR?

Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it

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