Bioconductor DNA Methylation

Showing : DNA Methylation • reset

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940

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minfi cell proportion estimateCellCounts DNA Methylation

4.2 years ago grayapply2009 • 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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977

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medips medip-seq dna methylation dmr analysis

updated 5.5 years ago by Lukas Chavez ▴ 570 • written 5.5 years ago by mtefit • 0

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1.6k

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R gdc rna-seq dna methylation

updated 5.6 years ago by Sean Davis 21k • written 5.6 years ago by RichardJActon ▴ 50

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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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755

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differential variability dna methylation iEVORA DVP

6.1 years ago poojitha.stemcell ▴ 10

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1.1k

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rnbeads methylation methylationepic dna methylation

6.3 years ago gabrielrfries • 0

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1.1k

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dna methylation biseq

updated 6.4 years ago by Gordon Smyth 50k • written 6.4 years ago by ahmad.moousavi • 0

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1.8k

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tcgabiolinks dna methylation

updated 6.5 years ago by Marcel Ramos 700 • written 6.5 years ago by michaelwxf2012 • 0

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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 66k • written 6.6 years ago by skids121 • 0

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1.2k

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CNV minfi preprocessing dna methylation

7.2 years ago Thomas • 0

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989

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microarray HM450 dna methylation cohcap

updated 7.3 years ago by James W. MacDonald 66k • written 7.3 years ago by 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 66k • written 7.9 years ago by fleur_p90 • 0

13 results • Page 1 of 1

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Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720

Thank you, but now I have six black and six red boxes (3 black, 3 red, 3 black, 3 red) whereas for each timepoint I have two experimental v…

Comment: Slightly different count plots from R and spreadsheet by Michael Love 42k

I added `col` so you can see the different groups. I just want you to be able to see the raw data so you can infer which plot is correct.

Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720

Thank you, the code you provided gives boxplots for each data-point for pooled samples?

Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman by xuz • 0

Could you try the following code and see whether you have any errors mf="MouseMethylation-12v1-0_A2.csv" manifest=readmanifest(mf) What …

Answer: Slightly different count plots from R and spreadsheet by Michael Love 42k

I'm gonna guess something went wrong in libreoffice. Try also ``` with(prb1, plot(timepoint, count, col=as.integer(ln))) ```

Votes

Including squared covariates to account for non-linear dependencies in differential gene expression analysis

DESeq2 DE gene expression of scRNA-seq pseudobulk

Answer: Multiple factor DSEq2 result generates weird volcano plot

DESeq2 for single cell pseudobulk processing

Simultaneously adding two different covariates in the model gives error in DESeq2.

Awards • All

Centurion to boczniak767 ▴ 720