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BSgenome BSgenome.Hsapiens.UCSC.hg38 Offline

updated 3 months ago by James W. MacDonald 68k • written 3 months ago by firestar ▴ 20

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KEGG R offline Pathway Enrichment

updated 5.0 years ago by Gordon Smyth 52k • written 5.4 years ago by omarrafiqued ▴ 50

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updated 9.8 years ago by Martin Morgan 25k • written 9.8 years ago by liangxinming ▴ 10

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Answer: WGCNA with paired samples by Ivo • 0

You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …

Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k

The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.

Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0

I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…

Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k

VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…

Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k

It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…

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Answer: normalizatino of dna methylation EPIC data

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