annotatedGenome	annotatedGenome-class
annotatedGenome-class	annotatedGenome-class
as.list,denovoGenomeExpr-method	denovoGeneExpr-class
calcDenovo	calcDenovo
calcExp	calcExp
coef,modelPriorAS,ANY,ANY,ANY-method	modelPriorAS-class
coef,modelPriorAS-method	modelPriorAS-class
coef,simulatedSamples-method	simulatedSamples-class
createDenovoGenome	procGenome
denovoExpr	denovoExpr
denovoGeneExpr-class	denovoGenomeExpr-class
denovoGenomeExpr-class	denovoGeneExpr-class
exprs,simulatedSamples-method	simulatedSamples-class
genePlot	genePlot
genePlot,CompressedIRangesList,ANY,ANY,ANY,ANY-method	genePlot
genePlot,GRanges,ANY,ANY,ANY,ANY-method	genePlot
genePlot,GRangesList,ANY,ANY,ANY,ANY-method	genePlot
genePlot,IRanges,ANY,ANY,ANY,ANY-method	genePlot
genePlot,IRangesList,ANY,ANY,ANY,ANY-method	genePlot
genePlot,missing,character,annotatedGenome,GRanges,ExpressionSet-method	genePlot
genePlot,missing,character,annotatedGenome,missing,missing-method	genePlot
genePlot,missing,character,annotatedGenome,procBam,ExpressionSet-method	genePlot
genePlot,missing,character,annotatedGenome,procBam,missing-method	genePlot
genePlot-methods	genePlot
getChr	getIsland
getChr,character,missing,missing,annotatedGenome-method	getIsland
getChr,missing,character,missing,annotatedGenome-method	getIsland
getChr,missing,missing,character,annotatedGenome-method	getIsland
getChr,missing,missing,missing,annotatedGenome-method	getIsland
getChr-method	getIsland
getDistrs	getDistrs
getIsland	getIsland
getIsland,character,missing,annotatedGenome-method	getIsland
getIsland,missing,character,annotatedGenome-method	getIsland
getNreads	getNreads
getNreads,pathCounts-method	getNreads
getReads	getReads
getReads,procBam-method	getReads
getRoc	getRoc
getRoc,logical,logical-method	getRoc
getRoc,matrix,matrix-method	getRoc
getRoc,numeric,numeric-method	getRoc
hg19DB	hg19DB
K562.r1l1	K562.r1l1
lines	plot-methods
lines,readDistrs-method	plot-methods
mergeBatches	mergeBatches
mergeBatches,ExpressionSet,ExpressionSet-method	mergeBatches
mergeBatches,ExpressionSet,simulatedSamples-method	mergeBatches
mergeExp	mergeExp
modelPrior	modelPrior
modelPriorAS-class	modelPriorAS-class
names,denovoGenomeExpr-method	denovoGenomeExpr-class
pathCounts	pathCounts
pathCounts,list-method	pathCounts
pathCounts,procBam-method	pathCounts
pathCounts-class	pathCounts-class
pathCounts-method	pathCounts
plot	plot-methods
plot,readDistrs,ANY-method	plot-methods
plotExpr	plotExpr
plotExpr,denovoGeneExpr-method	plotExpr
plotExpr-methods	plotExpr
plotPriorAS	plotPriorAS
plotPriorAS,modelPriorAS-method	plotPriorAS
plotPriorAS-methods	plotPriorAS
posprob	denovoGenomeExpr-class
posprob,denovoGeneExpr-method	denovoGenomeExpr-class
probNonEquiv	probNonEquiv
procBam	procBam
procBam,list,logical,integer,logical,character-method	procBam
procBam,list,logical,integer,logical,missing-method	procBam
procBam,list,logical,integer,missing,missing-method	procBam
procBam,list,logical,missing,logical,missing-method	procBam
procBam,list,logical,missing,missing,missing-method	procBam
procBam,list,missing,integer,logical,missing-method	procBam
procBam,list,missing,integer,missing,missing-method	procBam
procBam,list,missing,missing,logical,missing-method	procBam
procBam,list,missing,missing,missing,missing-method	procBam
procBam,list,missing,numeric,missing,missing-method	procBam
procBam-class	procBam-class
procBam-method	procBam
procGenome	procGenome
procGenome,GRanges,ANY-method	procGenome
procGenome,GRanges-method	procGenome
procGenome,TranscriptDb,ANY-method	procGenome
procGenome,TranscriptDb-method	procGenome
quantileNorm	quantileNorm
quantileNorm,ExpressionSet-method	quantileNorm
quantileNorm,matrix-method	quantileNorm
relativeExpr	calcDenovo
relexprByGene	relexprByGene
rmShortInserts	rmShortInserts
show,annotatedGenome-method	annotatedGenome-class
show,denovoGeneExpr-method	denovoGenomeExpr-class
show,denovoGenomeExpr-method	denovoGeneExpr-class
show,modelPriorAS-method	modelPriorAS-class
show,pathCounts-method	pathCounts-class
show,procBam-method	procBam-class
show,simulatedSamples-method	simulatedSamples-class
simMultSamples	simMultSamples
simReads	simReads
simulatedSamples-class	simulatedSamples-class
splitGenomeByLength	splitGenomeByLength
subsetGenome	subsetGenome
subsetGenome,character,missing,annotatedGenome-method	subsetGenome
subsetGenome,missing,character,annotatedGenome-method	subsetGenome
subsetGenome-methods	subsetGenome
transcripts	transcripts
transcripts,character,missing,annotatedGenome-method	transcripts
transcripts,missing,character,annotatedGenome-method	transcripts
txLength	txLength-methods
txLength,character,missing,annotatedGenome-method	txLength-methods
txLength,missing,character,annotatedGenome-method	txLength-methods
txLength,missing,data.frame,annotatedGenome-method	txLength-methods
txLength,missing,missing,annotatedGenome-method	txLength-methods
txLength-methods	txLength-methods
variants	denovoGenomeExpr-class
variants,denovoGeneExpr-method	denovoGenomeExpr-class
variants,denovoGenomeExpr-method	denovoGenomeExpr-class
variants<-	denovoGenomeExpr-class
variants<-,denovoGeneExpr-method	denovoGenomeExpr-class
wrapKnown	wrapKnown
[,denovoGeneExpr,ANY,ANY,ANY-method	denovoGenomeExpr-class
[,denovoGenomeExpr,ANY,ANY,ANY-method	denovoGeneExpr-class
[,modelPriorAS,ANY,ANY,ANY-method	modelPriorAS-class
[,simulatedSamples,ANY,ANY,ANY-method	simulatedSamples-class
[,simulatedSamples,missing,index,missing-method	simulatedSamples-class
[[,denovoGeneExpr,ANY,ANY,ANY-method	denovoGenomeExpr-class
[[,denovoGeneExpr,ANY,ANY-method	denovoGenomeExpr-class
[[,denovoGenomeExpr,ANY,ANY-method	denovoGenomeExpr-class
[[,denovoGenomeExpr-method	denovoGeneExpr-class
