Bioconductor DGEList

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597

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edgeR Bioconductor Dseq2 dgelist

updated 16 months ago by Gordon Smyth 50k • written 16 months ago by Fiona • 0

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824

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factors edgeR setup DGELIst

updated 2.9 years ago by Gordon Smyth 50k • written 2.9 years ago by Alex • 0

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1.7k

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edger DGElist

updated 5.0 years ago by Gordon Smyth 50k • written 5.0 years ago by naser.sadri • 0

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1.7k

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dgelist edger RnaSeqGeneEdgeRQL

updated 5.7 years ago by Gordon Smyth 50k • written 5.7 years ago by Kevin • 0

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2.0k

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edgeR summarizedexperiment dgelist

6.0 years ago aljoscha.leusmann • 0

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910

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tree bootstrap dgelist plotmds

6.1 years ago Larry K. • 0

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2.2k

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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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3.6k

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edger DGEList org.hs.eg.db gene annotation

updated 2.6 years ago by IIart.hubII • 0 • written 6.4 years ago by svlachavas ▴ 830

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3.0k

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egder dgelist group rnaseq

updated 6.5 years ago by Aaron Lun ★ 28k • written 6.5 years ago by fawazfebin ▴ 60

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3.1k

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DGElist filter edgeR

updated 6.8 years ago by Gordon Smyth 50k • written 6.8 years ago by alakatos ▴ 130

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2.4k

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edger raw reads TMM normalised values DGEList differential gene expression

updated 7.7 years ago by Steve Lianoglou ★ 13k • written 7.7 years ago by benedict.ng ▴ 20

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6.6k

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edger subsetting dgelist

updated 7.7 years ago by Gordon Smyth 50k • written 7.7 years ago by mnaymik ▴ 10

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20k

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edgeR row.names DGEList

9.2 years ago ccheung • 0

13 results • Page 1 of 1

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Comment: DESeq2 setting significant p-value by Michael Love 41k

It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.

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 …

Votes

Using GRanges and IRanges to simply get all chromosome data

A: Using GRanges and IRanges to simply get all chromosome data

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

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

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