Bioconductor NA

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EdgeR rnaseq NA

updated 9.6 years ago by Aaron Lun ★ 28k • written 9.6 years ago by elliott77 • 0

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snpStats BioConductor LD Linkage Disequilibrium NA

9.2 years ago remi.tournebize ▴ 10

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rtracklayer NA BED getseq

8.4 years ago Dimitris Polychronopoulos ▴ 80

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Gviz Plot NA graph Job

updated 8.7 years ago by James W. MacDonald 65k • written 8.7 years ago by Vinicius Henrique da Silva ▴ 40

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graphics confidence interval NA

updated 8.5 years ago by James W. MacDonald 65k • written 8.5 years ago by Vinicius Henrique da Silva ▴ 40

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gwastools lrr baf NA

updated 8.4 years ago by Stephanie M. Gogarten ▴ 870 • written 8.4 years ago by Vinicius Henrique da Silva ▴ 40

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deseq2 NA cooksCutoff

updated 8.1 years ago by Michael Love 41k • written 8.1 years ago by colaneri ▴ 30

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pvalue NA R DESeq2

updated 2.4 years ago by ATpoint ★ 4.0k • written 2.4 years ago by Johan Largo • 0

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reportingtools deseq2 NA pvalue

updated 7.8 years ago by Michael Love 41k • written 7.8 years ago by NMostajo ▴ 10

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deseq2 cook NA

updated 9.5 years ago by Michael Love 41k • written 9.5 years ago by skiaphrene ▴ 10

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qCount QuasR NA

updated 3.7 years ago by Michael Stadler ▴ 350 • written 3.7 years ago by jabbar_campbell • 0

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IRanges GRanges NA

updated 18 months ago by ATpoint ★ 4.0k • written 18 months ago by Timucin • 0

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edger dgelist NA egsea

updated 6.2 years ago by Gordon Smyth 50k • written 6.2 years ago by belmore • 0

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deseq2 coldata NA

updated 5.7 years ago by Michael Love 41k • written 5.7 years ago by t.kuilman ▴ 170

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methylkit normalizecoverage NA

updated 5.5 years ago by altuna akalin ▴ 20 • written 5.5 years ago by GFM ▴ 20

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limma mass spec na

updated 5.1 years ago by Gordon Smyth 50k • written 5.1 years ago by reubenmcgregor88 • 0

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rtracklayer NA

7.6 years ago Dario Strbenac ★ 1.5k

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parody r NA

9.1 years ago upendrakumar.devisetty • 0

18 results • Page 1 of 1

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Comment: Input Question for deseq.r by ATpoint ★ 4.0k

It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…

Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k

In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …

Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k

```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…

Comment: DESeq2 setting significant p-value by Dev • 0

after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …

Comment: DESeq filtering specific to contrasts by Carlin95 • 0

But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…

Votes

Comment: Reading huge bismark coverage files using bbseq::read.bismark

Answer: Reading huge bismark coverage files using bbseq::read.bismark

Answer: How many of my genes from my gene list are in each KEGG pathway?

Comment: Light difference when using coef vs omit a group when compare 3 groups.

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