analyzeComparative	analyzeComparative
analyzeQuantification	analyzeQuantification
ce.colAnnot	ChrEpi
ce.control	ChrEpi
ce.dnaCounts	ChrEpi
ce.rnaCounts	ChrEpi
ChrEpi	ChrEpi
controls	MpraObject
controls,MpraObject-method	MpraObject
dnaAnnot	MpraObject
dnaAnnot,MpraObject-method	MpraObject
dnaCounts	MpraObject
dnaCounts,MpraObject-method	MpraObject
dnaDepth	MpraObject
dnaDepth,MpraObject-method	MpraObject
estimateDepthFactors	estimateDepthFactors
extractModelParameters_DNA	extractModelParameters
extractModelParameters_RNA	extractModelParameters
getAlpha	getAlpha
getDistrParam_DNA	getDistrParam
getDistrParam_RNA	getDistrParam
getFits_DNA	getFits_DNA
getFits_RNA	getFits_RNA
getModelParameters_DNA	extractModelParameters
getModelParameters_RNA	extractModelParameters
model	MpraObject
model,MpraObject-method	MpraObject
MpraObject	MpraObject
MpraObject,matrix-method	MpraObject
MpraObject,SummarizedExperiment-method	MpraObject
rnaAnnot	MpraObject
rnaAnnot,MpraObject-method	MpraObject
rnaCounts	MpraObject
rnaCounts,MpraObject-method	MpraObject
rnaDepth	MpraObject
rnaDepth,MpraObject-method	MpraObject
rowAnnot	MpraObject
rowAnnot,MpraObject-method	MpraObject
setDepthFactors	setDepthFactors
setModel	setModel
simulateMPRA	simulateMPRA
testCoefficient	testCoefficient
testEmpirical	testEmpirical
testLrt	testLrt
