Bioconductor ColData

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1.1k

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DESeq2 design coldata

updated 16 months ago by swbarnes2 ★ 1.4k • written 16 months ago by arfranco ▴ 130

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1.2k

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ColData pheatmap DESeq2

written 2.2 years ago by dania.khalid • 0

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2.0k

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SingleCellExperiment colData rename

updated 2.6 years ago by Basti ▴ 780 • written 2.6 years ago by achoppe ▴ 10

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883

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BiSeq Coldata

5.3 years ago akhaira • 0

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2.2k

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deseq2 levels factor colData

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by ariel ▴ 20

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50k

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deseq2 coldata

updated 6.8 years ago by swbarnes2 ★ 1.4k • written 6.8 years ago by mjrarcher ▴ 10

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4.2k

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variantannotation coldata

updated 7.0 years ago by Valerie Obenchain ★ 6.8k • written 7.0 years ago by lvclark ▴ 10

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4.8k

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deseq2 coldata NA

updated 13 months ago by Michael Love 43k • written 7.1 years ago by t.kuilman ▴ 170

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2.0k

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multiassayexperiment colData

updated 7.8 years ago by Levi Waldron ★ 1.1k • written 7.8 years ago by Lluís Revilla Sancho ▴ 760

9 results • Page 1 of 1

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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?

Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0

Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…

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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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