Bioconductor Dna methylation

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1.5k

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minfi cell proportion estimateCellCounts DNA Methylation

5.9 years ago grayapply2009 • 0

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3.2k

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normalization DNA methylation WGCNA

updated 6.7 years ago by Peter Langfelder ★ 3.0k • written 6.7 years ago by enora.fremy • 0

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1.5k

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medips medip-seq dna methylation dmr analysis

updated 7.2 years ago by Lukas Chavez ▴ 570 • written 7.2 years ago by mtefit • 0

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2.4k

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R gdc rna-seq dna methylation

updated 7.3 years ago by Sean Davis 21k • written 7.3 years ago by RichardJActon ▴ 50

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2.1k

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minfi normalization outliers dna methylation densityplot

7.6 years ago peter.fransquet • 0

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1.1k

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differential variability dna methylation iEVORA DVP

7.8 years ago poojitha.stemcell ▴ 10

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1.5k

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rnbeads methylation methylationepic dna methylation

8.0 years ago gabrielrfries • 0

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1.5k

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dna methylation biseq

updated 8.1 years ago by Gordon Smyth 53k • written 8.1 years ago by ahmad.moousavi • 0

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2.6k

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tcgabiolinks dna methylation

updated 8.2 years ago by Marcel Ramos 700 • written 8.2 years ago by michaelwxf2012 • 0

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2.6k

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dna methylation illimina 450k methylation beta M significance

updated 8.4 years ago by James W. MacDonald 68k • written 8.4 years ago by skids121 • 0

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1.7k

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CNV minfi preprocessing dna methylation

8.9 years ago Thomas • 0

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microarray HM450 dna methylation cohcap

updated 9.1 years ago by James W. MacDonald 68k • written 9.1 years ago by poojitha.stemcell ▴ 10

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1.5k

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minfi bumphunter DNA methylation illumina450k

updated 9.7 years ago by James W. MacDonald 68k • written 9.7 years ago by fleur_p90 • 0

13 results • Page 1 of 1

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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k

I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0

Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…

Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0

Hello, I was also wondering about the same issue. Did you figure it out?

Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0

FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…

Votes

Answer: Subsetting data verses contrasts [DESeq2]?

A: WGCNA differences two groups 10 replicates each group

A: WGCNA sample size minimum: why?

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name

Answer: Can you colour dendrogram branch clusters in pheatmap?

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Popular Question to Peter Hickey ▴ 760