Bioconductor MethylKit

Showing : methylKit • reset

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1.7k

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methylKit

6.9 years ago kamal.fartiyal84 ▴ 10

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1.7k

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methylKit

updated 6.8 years ago by altuna akalin ▴ 20 • written 6.8 years ago by ch8316f5eyu • 0

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1.6k

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methylKit bioconductor

updated 7.7 years ago by Martin Morgan 25k • written 7.7 years ago by tangming2005 ▴ 190

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1.6k

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methylkit Tutorial

updated 6.4 years ago by Martin Morgan 25k • written 6.4 years ago by s1432985 • 0

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1.5k

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GenomicRanges methylKit S4Vectors

updated 2.1 years ago by James W. MacDonald 65k • written 2.1 years ago by hasche • 0

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1.2k

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methylkit normalizecoverage NA

updated 5.5 years ago by altuna akalin ▴ 20 • written 5.5 years ago by GFM ▴ 20

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1.2k

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methylkit

updated 2.6 years ago by alex.gos90 ▴ 10 • written 2.9 years ago by hasche • 0

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1.1k

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R bioconductor methylation methylkit

updated 5.8 years ago by altuna akalin ▴ 20 • written 5.8 years ago by nilaycan • 0

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1.1k

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annotateWithGeneParts methylKit

2.6 years ago tanmayroy1979 ▴ 20

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1.1k

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methylation methylKit bsseq

updated 2.6 years ago by alex.gos90 ▴ 10 • written 2.8 years ago by ag1805x ▴ 80

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659

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methyl methylKit

2.1 years ago hasche • 0

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589

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methRead methylkit

16 months ago liulip • 0

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453

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methylKit

9 months ago Andrés • 0

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227

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methylKit

updated 29 days ago by James W. MacDonald 65k • written 4 weeks ago by CHEN • 0

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128

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methylKit

29 days ago Modoc Kesner ▴ 10

15 results • Page 1 of 1

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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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