User: zoe.ward

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zoe.ward0
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Posts by zoe.ward

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NCBI hg38 transcript annotation package GenomicFeatures
... Hi all,   I'm very new to using GenomicFeatures and I'm trying to download a NCBI hg38 transcript annotation package (I want to use the built in functions such as promoters() etc). Can someone direct me to where I can get this? I have tried > makeTxDbFromBiomart but this isn't working for m ...
genomicfeatures written 5 months ago by zoe.ward0 • updated 5 months ago by James W. MacDonald49k
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DEXSeq and DRIMSeq on paired samples?
... I have 85 paired samples i.e. before and after ischemia so my question is how would I run the DEXSeq and DRIMSeq on paired samples? I’ve had a look in the relevant vignettes but cannot find any example of paired analysis. I have a design matrix like so: sample_id cond pair ...
dexseq drimseq written 5 months ago by zoe.ward0 • updated 5 months ago by gosia.nowicka40
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pair wise ballgown
... I have tried to find a beginners guide/tutorial on how to do a paired analysis in Ballgown. I have several samples pre and post treatment: ID<- seq(1,170, by=1) cond<-rep(c("post","pre"),85) pair<- rep(1:85, each = 2) design_matrix <- data.frame(id=ID,cond=cond, pair=factor(pair)) ...
differential expression ballgown written 9 months ago by zoe.ward0

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