I am using a Bioconductor package called spliceR to identify any alternative splicing events in two samples. For this purpose, I am following the basic steps suggested in the paper.
for CDS annotation I am downloaded
library(BSgenome.Hsapiens.UCSC.hg19) require("BSgenome.Hsapiens.UCSC.hg19",character.only=T) ucscCDS <- getCDS(selectedGenome = "hg19",repoName = "UCSC") ## Retrieving CDS tables for UCSC...
It has been more than 24 hours but the retrieving CDS tables step is still running. I am uncertain if this problem is related to the system or to the repository.