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iranges ifelse package namespace export

updated 7.1 years ago by James W. MacDonald 68k • written 7.1 years ago by dalibor.miklik • 0

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seqlm IRanges R namespace dmr analysis

8.6 years ago calen.p.ryan • 0

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edgeR namespace

updated 8.9 years ago by Gordon Smyth 52k • written 8.9 years ago by BharathAnanth ▴ 80

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targetscan namespace

updated 9.5 years ago by James W. MacDonald 68k • written 9.5 years ago by Assa Yeroslaviz ★ 1.5k

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Answer: cameraPR() non directional test by Gordon Smyth 52k

Yes, you can still do non-directional tests using cameraPR(), but it's not quite as easy as it was using the original camera() function as …

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…

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Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu

Answer: normalizatino of dna methylation EPIC data

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

Suggesting changing the "reply-to" field to the mailing list address.

Answer: UniProt.ws query for single UniRef90 ID takes several minutes

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