A Shiny/R app to display the Illumina human body map dataset. I have not included the expression data due to it's size (19Gb) but this should work with any RNA-seq data set analysed with a TopHat->Cufflinks->CuffDiff pipeline.

server.R

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() {
		if (!nzchar(input$gene))
			return()
		return(getGene(cuff,input$gene))
	})
	
	output$genePlot  = reactivePlot(function() { 
		myGene = getData()
		#fudge to stop shiny trying to plot NULL, which results in an ugly black square:
		if (is.null(myGene))
        		return(plot(1,type="n",bty="n",yaxt="n",xaxt="n",ylab="",xlab=""))
		x = data.frame(
			tissue = fpkm(myGene)$sample_name,
			fpkm=fpkm(myGene)$fpkm
		)
		print(ggplot(x,aes(fill=tissue,x=tissue,y=fpkm)) + geom_bar(position="dodge", stat="identity") + 
			labs(title=annotation(myGene)$gene_short_name))
	})  

	output$isoformPlot  = reactivePlot(function() { 
		myGene = getData()
		if (is.null(myGene))
			return(plot(1,type="n",bty="n",yaxt="n",xaxt="n",ylab="",xlab=""))
		trackList=list()
		myStart=min(features(myGene)$start)
		myEnd=max(features(myGene)$end)
		myChr=unique(features(myGene)$seqnames)
		genome='hg19'
		ideoTrack = IdeogramTrack(genome = genome, chromosome = myChr)
		axtrack=GenomeAxisTrack()
		genetrack=makeGeneRegionTrack(myGene)
		biomTrack=BiomartGeneRegionTrack(genome=genome,chromosome=as.character(myChr),
			start=myStart,end=myEnd,name="ENSEMBL",showId=T)
		trackList=c(trackList,ideoTrack,axtrack,genetrack,biomTrack)
		plotTracks(trackList,from=myStart-5000,to=myEnd+5000)
	})
		
	output$tissueIsoformPlot  = reactivePlot(function() { 
		myGene = getData()
		if (is.null(myGene))
			return(plot(1,type="n",bty="n",yaxt="n",xaxt="n",ylab="",xlab=""))
		x = data.frame(
			isoform = fpkm(isoforms(myGene))[fpkm(isoforms(myGene))$sample_name==input$tissue,]$isoform_id,
			fpkm=fpkm(isoforms(myGene))[fpkm(isoforms(myGene))$sample_name==input$tissue,]$fpkm
		)
		print(ggplot(x,aes(fill=isoform,x=isoform,y=fpkm)) + geom_bar(position="dodge", stat="identity") + 
		labs(title=input$tissue) + opts(axis.text.x=theme_text(angle=90, hjust=1)))
	})
})

ui.R

library(shiny)

# Define UI 
shinyUI(pageWithSidebar(
  
  # Application title
	headerPanel("Human Body Map"),
  
	sidebarPanel(
		textInput("gene", label="Gene", value = ""),
		submitButton("Submit"),

		conditionalPanel(condition="input.gene.length > 0",
			br(),
			selectInput("tissue", "Select a tissue to view isoform expression in:",
				list("adipose" = "adipose", 
					"adrenal" = "adrenal", 
					"brain" = "brain",
					"breast" = "breast",
					"colon" = "colon",
					"heart" = "heart",
					"kidney" = "kidney",
					"liver" = "liver",
					"lung" = "lung",
					"lymph" = "lymph",
					"lymphocyte" = "lymphocyte",
					"muscle" = "muscle",
					"ovary" = "ovary",
					"prostate" = "prostate",
					"testes" = "testes",
					"thyroid" = "thyroid")
			)
		)
	),

	mainPanel(
		conditionalPanel(condition="$('html').hasClass('shiny-busy')",img(src="http://i1215.photobucket.com/albums/cc508/nawel12/loading.gif")),
		plotOutput("genePlot"),
		plotOutput("isoformPlot"),
		plotOutput("tissueIsoformPlot")
	)

))