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IRanges GRanges NA

updated 2.6 years ago by ATpoint ★ 4.8k • written 2.6 years ago by Timucin • 0

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pvalue NA R DESeq2

updated 3.4 years ago by ATpoint ★ 4.8k • written 3.4 years ago by Johan Largo • 0

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qCount QuasR NA

updated 4.8 years ago by Michael Stadler ▴ 350 • written 4.8 years ago by jabbar_campbell • 0

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limma mass spec na

updated 6.1 years ago by Gordon Smyth 52k • written 6.1 years ago by reubenmcgregor88 • 0

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methylkit normalizecoverage NA

updated 6.5 years ago by altuna akalin ▴ 20 • written 6.5 years ago by GFM ▴ 20

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deseq2 coldata NA

updated 8 months ago by Michael Love 43k • written 6.7 years ago by t.kuilman ▴ 170

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edger dgelist NA egsea

updated 7.2 years ago by Gordon Smyth 52k • written 7.2 years ago by belmore • 0

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rtracklayer NA

8.6 years ago Dario Strbenac ★ 1.6k

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reportingtools deseq2 NA pvalue

updated 8.8 years ago by Michael Love 43k • written 8.8 years ago by NMostajo ▴ 10

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deseq2 NA cooksCutoff

updated 9.1 years ago by Michael Love 43k • written 9.1 years ago by colaneri ▴ 30

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gwastools lrr baf NA

updated 9.4 years ago by Stephanie M. Gogarten ▴ 890 • written 9.4 years ago by Vinicius Henrique da Silva ▴ 40

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rtracklayer NA BED getseq

9.4 years ago Dimitris Polychronopoulos ▴ 80

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graphics confidence interval NA

updated 9.6 years ago by James W. MacDonald 68k • written 9.6 years ago by Vinicius Henrique da Silva ▴ 40

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Gviz Plot NA graph Job

updated 9.8 years ago by James W. MacDonald 68k • written 9.8 years ago by Vinicius Henrique da Silva ▴ 40

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parody r NA

10.1 years ago upendrakumar.devisetty • 0

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snpStats BioConductor LD Linkage Disequilibrium NA

10.2 years ago remi.tournebize ▴ 10

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deseq2 cook NA

updated 10.5 years ago by Michael Love 43k • written 10.5 years ago by skiaphrene ▴ 10

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EdgeR rnaseq NA

updated 10.6 years ago by Aaron Lun ★ 28k • written 10.6 years ago by elliott77 • 0

18 results • Page 1 of 1

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Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0

This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/

Comment: Filtering after DESeq by ATpoint ★ 4.8k

The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …

Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k

All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…

Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k

> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…

Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k

Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…

Votes

Answer: DiffBind; Error: No sites have activity greater than filter value

DiffBind; Error: No sites have activity greater than filter value

remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline

How to remove X & Y chromosome genes from RNAseq data

Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?

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Popular Question to Dario Strbenac ★ 1.6k