Bioconductor DES

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311

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DESeq2 des

updated 6 months ago by James W. MacDonald 67k • written 6 months ago by Atul K. • 0

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1.1k

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 9 months ago by James W. MacDonald 67k • written 9 months ago by Alexandre • 0

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327

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Des DESeq2

updated 9 months ago by hemantcnaik • 0 • written 9 months ago by Sahar • 0

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527

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DESeq2 DEs

10 months ago feather-W • 0

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687

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DESeq2 des

updated 2.2 years ago by Michael Love 43k • written 2.2 years ago by Devin • 0

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764

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DES DESIGN

updated 2.3 years ago by Michael Love 43k • written 2.3 years ago by mike • 0

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876

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DESeq2 DES

updated 4.1 years ago by Michael Love 43k • written 4.1 years ago by heikki.sarin ▴ 10

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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0

Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…

Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740

Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…

Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10

Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…

Comment: EdgeR Biological CVs by ATpoint ★ 4.6k

"Joseph" is a spam bot...

Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k

GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…

Votes

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

Answer: Error in download.file for TCGAutils::symbolsToRanges

Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?

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