Bioconductor Splicesites

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rtracklayer spliceSites rtracklayer spliceSites

updated 13.8 years ago by Sean Davis 21k • written 13.8 years ago by Johannes Waage ▴ 50

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ciri splicing splicesites

updated 3.7 years ago by lhddiallo • 0 • written 5.3 years ago by csijst • 0

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Answer: Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray by nehagoyal6397 • 0

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Comment: filtering out lowly expressed genes by groups by James W. MacDonald 63k

You might want to filter first though. ``` fun <- function(deseqobj, contvec, cutoff) { lildds <- dds[rowMeans(assays(deseqobj…

Answer: filtering out lowly expressed genes by groups by James W. MacDonald 63k

Something like ``` results(dds, c("condition","T0_unstim_CRWnP","T0_unstim_HC"))[rowMeans(assays(dds, "counts")[,colData(dds)$condition…

Comment: Representation of self-loops and the calculation of degrees by Vincent J. Carey, Jr. 6.7k

> packageVersion("graph") [1] '1.79.2' > gn <- graphNEL(nodes=c('A','B'), edgeL=list(A=c('A','B'), B=c('A')), edgemode='undirec…

Comment: filtering out lowly expressed genes by groups by sohail.mbio ▴ 10

My question is how to avoid these DEGs? There are so many DEGs that are not actually expressed at T0. Is there any filter ? my current code…