addBamData	addBamData
addDataToReadset	addDataToReadset
addExperimentsToReadset	addExperimentsToReadset
allCamelMeasuresForRegion	gRanges2CamelMeasures
averageND	averageND
bam2sig	bam2sig
buildDESeq	buildDESeq
buildDGEList	buildDGEList
combineND	averageND
densityNormalize	normalizations
diff_area	measures
diff_derivative_area	measures
distrCOVPlot	NDplots
distrCOVPlotg	NDplots
distribs	NucleotideDistr-class
distrSIPlot	NDplots
findRegionsAsIR	findRegionsAsIR
findRegionsAsND	findRegionsAsND
fiveCol2GRanges	fiveCol2GRanges
gcoverage	regionCoverage
geneInChromosome	geneInChromosome
generatorAdd	generators
generatorAddSquare	generators
generatorMultiply	generators
generatorPeak	generators
generatorSynth	generators
generatorTrunc	generators
getBamData	getBamData
getCoverageFromRS	getCoverageFromRS
getData	getData
getDistr	NucleotideDistr-class
getExpDescription	getExpDescription
getFCFromND	getFCFromND
getSIFromND	getSIFromND
getSumsExp	getSumsExp
ghistogram	plotGeneCoverage
globalCountsNormalize	normalizations
gRanges2CamelMeasures	gRanges2CamelMeasures
hump_diff1	measures
hump_diff2	measures
ks_test	measures
log2ND	averageND
min_maxNormalize	normalizations
newNuctleotideDistr	NucleotideDistr-class
newSeqReads	SeqReds
newSeqReadsFromGene	SeqReds
normalizeBySum	normalizeBySum
NucleotideDistr-class	NucleotideDistr-class
parseGff3	parseGff3
plotCoverageHistogram	plotGeneCoverage
plotExonCoverage	plotGeneCoverage
plotGeneCoverage	plotGeneCoverage
plotGeneExonCoverage	plotGeneCoverage
plotRegionCoverage	plotGeneCoverage
plotSI	plotGeneCoverage
pp_derivative_plot	measures
pp_plot	measures
qq_derivative_plot	measures
qq_plot	measures
readsInRange	readsInRange
regionBasedCoverage	regionBasedCoverage
regionCoverage	regionCoverage
regionmining	findRegionsAsND
RleList2matrix	RleList2matrix
rs.list	rs.list
sample_data_rnaSeqMap	rs.list
SeqReads	SeqReds
SeqReads-class	SeqReds
setData	setData
setSAXPYData	setSAXPYData
setSpecies	setSpecies
simplePlot	simplePlot
spaceInChromosome	spaceInChromosome
splicingind	getSIFromND
standarizationNormalize	normalizations
sumND	averageND
