Bioconductor Rrbs

Showing : rrbs • reset

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1.5k

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edgeR model-selection RRBS mixture-experiment

4.4 years ago ingerslev • 0

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1.2k

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MethylCC RRBS cord blood

5.1 years ago weichen-cls • 0

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1.0k

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Biseq Methylation DMP DMR RRBS

5.1 years ago i.s.castanho • 0

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924

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biseq betaRegression RRBS Methylation

5.5 years ago i.s.castanho • 0

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2.8k

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edgeR rrbs

updated 6.7 years ago by Gordon Smyth 53k • written 6.7 years ago by ingerslev • 0

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3.2k

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methykit rrbs

updated 7.3 years ago by Mike Smith ★ 6.6k • written 7.3 years ago by bekah ▴ 40

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1.9k

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edgeR methyation RRBS

updated 7.6 years ago by Gordon Smyth 53k • written 7.6 years ago by osa.zuta ▴ 40

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1.4k

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biseq RRBS betaregression

8.4 years ago l.eijssen • 0

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2.5k

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sva RRBS

updated 8.5 years ago by Jeff Leek ▴ 650 • written 8.5 years ago by mrodrigues.fernanda ▴ 10

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2.1k

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rrbs batch effect methylation sva

updated 8.9 years ago by dashbrook1 • 0 • written 10.1 years ago by GFM ▴ 20

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1.9k

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limma rrbs bsseq

updated 9.2 years ago by Aaron Lun ★ 29k • written 9.3 years ago by nhejazi • 0

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2.6k

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biseq RRBS SAAP-BS coverage

10.4 years ago maria.maqueda • 0

12 results • Page 1 of 1

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Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k

Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…

Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k

There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?

Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k

What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…

Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…

Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740

@atpoint Should I first standardise data and then average replicates?

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Answer: Limpa Pipeline Order

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

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