User: zoe.ward

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zoe.ward0
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Posts by zoe.ward

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DESEQ2 for circRNA normalisation
... I’m a PhD student struggling to get my head around what I do to normalise my circRNA data (have tried to look at all of the related posts on various sites) I am using DESEQ2 for differential analysis and have my gene matrix counts for the linear genes: [1] dds <- DESeqDataSetFromTximport ...
deseq2 circrna normalisation written 2 hours ago by zoe.ward0
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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 14 months ago by zoe.ward0 • updated 14 months ago by James W. MacDonald52k
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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 14 months ago by zoe.ward0 • updated 14 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 18 months ago by zoe.ward0

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