IntEREst-package	IntEREst-package
addAnnotation	addAnnotation
annotateU12	annotateU12
attributes	attributes
boxplot,SummarizedExperiment-method	boxplot-method
boxplot-method	boxplot-method
buildSsTypePwms	buildSsTypePwms
counts,SummarizedExperiment-method	counts-method
counts-method	counts-method
counts.InterestResults	counts-method
deseqInterest	deseqInterest
DEXSeqIntEREst	DEXSeqIntEREst
exactTestInterest	exactTestInterest
getAnnotation	attributes
getRepeatTable	getRepeatTable
glmInterest	glmInterest
IntEREst	IntEREst-package
interest	interest
interest.sequential	interest.sequential
InterestResult	interestResult
interestResultIntEx	interestResultIntEx
intexBoxplot	boxplot-method
intexIndex	intexIndex
lfc	lfc
mdsChr22ExObj	mdsChr22ExObj
mdsChr22IntSpObj	mdsChr22IntSpObj
mdsChr22Obj	mdsChr22Obj
mergeInterestResult	mergeInterestResult
plot,SummarizedExperiment,ANY-method	plot-method
plot-method	plot-method
plot.InterestResult	plot-method
psi	psi
pwmU12db	pwmU12db
qlfInterest	qlfInterest
readInterestResults	readInterestResults
referencePrepare	referencePrepare
scaledRetention	attributes
subInterestResult	subInterestResult
treatInterest	treatInterest
u12	u12
u12Boxplot	u12Boxplot
u12BoxplotNb	u12BoxplotNb
u12DensityPlot	u12DensityPlot
u12DensityPlotIntron	u12DensityPlot
u12Index	u12Index
u12NbIndex	u12NbIndex
unionRefTr	unionRefTr
updateRowDataCol	updateRowDataCol
