Bioconductor Methylkit

Showing : methylkit • reset

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methylKit

updated 12 months ago by James W. MacDonald 68k • written 12 months ago by Satyanarayan • 0

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660

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methylKit

updated 15 months ago by alex.gos90 ▴ 10 • written 15 months ago by Krisztina • 0

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1.5k

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methylKit

updated 19 months ago by James W. MacDonald 68k • written 19 months ago by CHEN • 0

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585

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methylKit

19 months ago Modoc Kesner ▴ 10

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1.0k

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methylKit

2.2 years ago Andrés • 0

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997

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methRead methylkit

2.9 years ago liulip • 0

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1.1k

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methyl methylKit

3.6 years ago hasche • 0

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2.5k

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GenomicRanges methylKit S4Vectors

updated 3.6 years ago by James W. MacDonald 68k • written 3.6 years ago by hasche • 0

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1.8k

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methylkit

updated 4.0 years ago by alex.gos90 ▴ 10 • written 4.4 years ago by hasche • 0

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2.4k

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methylation methylKit bsseq

updated 4.0 years ago by alex.gos90 ▴ 10 • written 4.3 years ago by Arindam ▴ 80

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2.0k

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annotateWithGeneParts methylKit

4.1 years ago tanmayroy1979 ▴ 20

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1.8k

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methylkit normalizecoverage NA

updated 7.0 years ago by altuna akalin ▴ 20 • written 7.0 years ago by GFM ▴ 20

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1.7k

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R bioconductor methylation methylkit

updated 7.3 years ago by altuna akalin ▴ 20 • written 7.3 years ago by nilaycan • 0

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methylkit Tutorial

updated 7.9 years ago by Martin Morgan 25k • written 7.9 years ago by s1432985 • 0

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methylKit

updated 8.3 years ago by altuna akalin ▴ 20 • written 8.3 years ago by ch8316f5eyu • 0

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methylKit

8.4 years ago kamal.fartiyal84 ▴ 10

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methylKit bioconductor

updated 9.2 years ago by Martin Morgan 25k • written 9.2 years ago by tangming2005 ▴ 200

17 results • Page 1 of 1

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Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

Votes

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

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