Bioconductor DESeq2

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805

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DESeq2 RNASeq PrincipalComponent pcaExplorer

written 18 months ago by James • 0

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242

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DESeq2

updated 3 days ago by ATpoint ★ 4.2k • written 5 days ago by tjl • 0

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200

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DESeq2 ggplot2

7 days ago • updated 6 days ago boczniak767 ▴ 720

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142

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DESeq2 GSVA ssGSEA

updated 2 days ago by Robert Castelo ★ 3.3k • written 5 days ago by michelafrancesconi8 • 0

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115

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Seurat DESeq2 single-cell scRNA Pseudobulk

updated 2 days ago by Guido Hooiveld ★ 4.0k • written 3 days ago by Sara • 0

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114

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DESeq2 clinicaltraits Normalization batchnormalisation

5 days ago • updated 2 days ago sukeshinik5 • 0

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104

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DESeq2

1 day ago • updated 1 hour ago ennui • 0

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DESeq2

updated 1 hour ago by James W. MacDonald 66k • written 23 hours ago by boczniak767 ▴ 720

8 results • Page 1 of 1

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Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0

Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…

Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0

For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…

Answer: LRT, pairwise comparisons and p-value adjustment by James W. MacDonald 66k

The convention is to adjust only within comparisons. But as the analyst, that's your call.

Comment: Counter-directional LFC shrinkage by ennui • 0

Thank you for your response. The `ashr` shrinkage indeed preserves more of the original ranks in the data. So if I understand correctly, L…

Comment: Counter-directional LFC shrinkage by ennui • 0

I agree it looks offset (and weird). The data is from NGS, not RNAseq, but we still want to see relative abundance between conditions - I t…

Votes

Reduce the number of nodes appear in the cnetplot of clusterprofiler

A: DESeq2: add annotations (from data frame) to DESeqDataSet

Answer: Error in gseDO function

Comment: what the test method for enrichGO in clusterProfiler?

A: Comparison between two different group's pathway analysis results

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Popular Question to Guido Hooiveld ★ 4.0k