Bioconductor DNA Methylation

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1.6k

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R gdc rna-seq dna methylation

updated 5.5 years ago by Sean Davis 21k • written 5.5 years ago by RichardJActon ▴ 50

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1.8k

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tcgabiolinks dna methylation

updated 6.4 years ago by Marcel Ramos 690 • written 6.4 years ago by michaelwxf2012 • 0

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1.8k

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normalization DNA methylation WGCNA

updated 4.9 years ago by Peter Langfelder ★ 3.0k • written 4.9 years ago by enora.fremy • 0

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983

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microarray HM450 dna methylation cohcap

updated 7.3 years ago by James W. MacDonald 65k • written 7.3 years ago by poojitha.stemcell ▴ 10

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1.5k

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dna methylation illimina 450k methylation beta M significance

updated 6.6 years ago by James W. MacDonald 65k • written 6.6 years ago by skids121 • 0

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968

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medips medip-seq dna methylation dmr analysis

updated 5.4 years ago by Lukas Chavez ▴ 570 • written 5.4 years ago by mtefit • 0

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1.1k

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minfi normalization outliers dna methylation densityplot

5.8 years ago peter.fransquet • 0

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932

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minfi cell proportion estimateCellCounts DNA Methylation

4.1 years ago grayapply2009 • 0

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1.2k

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CNV minfi preprocessing dna methylation

7.1 years ago Thomas • 0

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1.1k

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dna methylation biseq

updated 6.3 years ago by Gordon Smyth 50k • written 6.3 years ago by ahmad.moousavi • 0

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1.0k

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rnbeads methylation methylationepic dna methylation

6.2 years ago gabrielrfries • 0

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746

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differential variability dna methylation iEVORA DVP

6.0 years ago poojitha.stemcell ▴ 10

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1.1k

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minfi bumphunter DNA methylation illumina450k

updated 7.9 years ago by James W. MacDonald 65k • written 7.9 years ago by fleur_p90 • 0

13 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!

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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

A: Print Differentially Expressed Exons From Dexseq Results

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