sidderb
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| library(shiny) | |
| library(deSolve) | |
| library(cummeRbund) | |
| # load cuffDiff data, must be in top dir and called cuffData.db: | |
| cuff = readCufflinks() | |
| shinyServer(function(input,output) { | |
| getData = reactive(function() { |
sidderb
/ strandedBamImport
Last active
March 15, 2016 05:44
Visualising stranded RNA-seq data with Gviz/Bioconductor
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| # A function to extract reads from a stranded RNA-seq BAM file. Intended to be used as a custom importFunction | |
| # in the DataTrack constructor of Bioconductor's Gviz package. With properly stranded data this allows the plotting | |
| # of coverage tracks from each strand of the genome. | |
| # | |
| # 6 Nov 2014 - bensidders at gmail dot com | |
| # | |
| # UPDATE: 10 Sep 2015: | |
| # The funciton can now plot data from libraries created in either orientation. Due to the manner in which Gviz calls | |
| # this function, you need to specify the library orientation with a global variable "libType" to be one of | |
| # "fr-firststrand" or "fr-secondstrand". |