Bioconductor Rrbs

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1.3k

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edgeR model-selection RRBS mixture-experiment

3.7 years ago ingerslev • 0

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1.1k

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MethylCC RRBS cord blood

4.5 years ago weichen-cls • 0

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923

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Biseq Methylation DMP DMR RRBS

4.5 years ago i.s.castanho • 0

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773

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biseq betaRegression RRBS Methylation

4.8 years ago i.s.castanho • 0

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2.4k

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edgeR rrbs

updated 6.0 years ago by Gordon Smyth 52k • written 6.0 years ago by ingerslev • 0

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2.7k

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methykit rrbs

updated 6.7 years ago by Mike Smith ★ 6.6k • written 6.7 years ago by bekah ▴ 40

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1.7k

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edgeR methyation RRBS

updated 7.0 years ago by Gordon Smyth 52k • written 7.0 years ago by osa.zuta ▴ 40

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1.3k

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biseq RRBS betaregression

7.8 years ago l.eijssen • 0

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2.1k

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sva RRBS

updated 7.8 years ago by Jeff Leek ▴ 650 • written 7.8 years ago by mrodrigues.fernanda ▴ 10

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1.9k

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rrbs batch effect methylation sva

updated 8.3 years ago by dashbrook1 • 0 • written 9.5 years ago by GFM ▴ 20

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1.7k

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limma rrbs bsseq

updated 8.6 years ago by Aaron Lun ★ 28k • written 8.6 years ago by nhejazi • 0

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2.3k

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biseq RRBS SAAP-BS coverage

9.7 years ago maria.maqueda • 0

12 results • Page 1 of 1

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Answer: DESeq2 analysis with transcript counts by ATpoint ★ 4.6k

You need to account for the inferential uncertainty of mapping, that is because transcripts of the same gene shared most exonic content, so…

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by James W. MacDonald 67k

How you analyze your data is up to you. But do note that Subset * Conditions implies that you want to find genes that respond to stimulus d…

Comment: MBDseq analysis using qsea package by kf • 0

Hi Matthias, Happy new year! I wondered if it is possible to retrieve normalized value from each samples? makeTable seems only return beta…

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Quang ▴ 10

Hi, James. I forgot to mention, but yes, I did run `DESeq2::DESeq()`. So, I ran `DESeq2::DESeqDataSetFromHTSeqCount`, then `DESeq2::DESeq()…

Answer: Why did PCA plots look exactly the same after adjusting for batch covariate in D by ATpoint ★ 4.6k

It's an FAQ in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-s…

Votes

Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?

A: Trajectory analysis for single cell sequencing

Answer: Annotation with org.Hs.eg.db Genome Build 38

Answer: Considerations behind the choice of RNAseq Differential Expression Analysis Tool

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Popular Question to Assa Yeroslaviz ★ 1.5k