sidderb

# 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".

sidderb

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() {