addAnnotationToTSR	addAnnotationToTSR-methods
addAnnotationToTSR,tssObject,character,numeric,numeric,numeric,character,character,logical-method	addAnnotationToTSR-methods
addTagCountsToTSR	addTagCountsToTSR-methods
addTagCountsToTSR,tssObject,character,numeric,numeric,logical-method	addTagCountsToTSR-methods
bedToTSS	bedToTSS-methods
bedToTSS,tssObject-method	bedToTSS-methods
createSummarizedExperiment	createSummarizedExperiment-methods
createSummarizedExperiment,tssObject,character,numeric,character-method	createSummarizedExperiment-methods
determineTSR	determineTSR-methods
determineTSR,tssObject,numeric,character,character,numeric,numeric-method	determineTSR-methods
detTSR	detTSR-methods
detTSR,tssObject,character,numeric,numeric,numeric-method	detTSR-methods
getBamDataFirstRead	getBamDataFirstRead-methods
getBamDataFirstRead,tssObject,numeric-method	getBamDataFirstRead-methods
getBamDataLastRead	getBamDataLastRead-methods
getBamDataLastRead,tssObject,numeric-method	getBamDataLastRead-methods
getFileNames	getFileNames-methods
getFileNames,tssObject-method	getFileNames-methods
getTitle	getTitle-methods
getTitle,tssObject-method	getTitle-methods
getTSRdata	getTSRdata-methods
getTSRdata,tssObject,character,numeric-method	getTSRdata-methods
getTSScountData	getTSScountData-methods
getTSScountData,tssObject,character,numeric-method	getTSScountData-methods
getTSStagData	getTSStagData-methods
getTSStagData,tssObject,numeric-method	getTSStagData-methods
gsq2bed	gsq2bed-methods
gsq2bed,character,character-method	gsq2bed-methods
importAnnotationExternal	importAnnotationExternal-methods
importAnnotationExternal,tssObject,character,character-method	importAnnotationExternal-methods
importAnnotationHub	importAnnotationHub-methods
importAnnotationHub,tssObject,character,character,character,character-method	importAnnotationHub-methods
inputToTSS	inputToTSS-methods
inputToTSS,tssObject-method	inputToTSS-methods
loadTSSobj	loadTSSobj-methods
loadTSSobj,character,character-method	loadTSSobj-methods
makeGRangesFromTSR	makeGRangesFromTSR-methods
makeGRangesFromTSR,tssObject,character,numeric-method	makeGRangesFromTSR-methods
mergeSampleData	mergeSampleData-methods
mergeSampleData,tssObject,numeric,numeric-method	mergeSampleData-methods
prcTSS	prcTSS
processTSS	processTSS-methods
processTSS,tssObject,numeric,character,logical-method	processTSS-methods
tagCountTSS	tagCountTSS
TSRchitectUsersGuide	TSRchitectUsersGuide
tsrCluster	tsrCluster
TSRmshapeIndex	TSRmshapeIndex
TSRshapeIndex	TSRshapeIndex
tssArrayProperties	tssArrayProperties
tssObject	tssObject
writeTSR	writeTSR-methods
writeTSR,tssObject,character,numeric,character,logical,character-method	writeTSR-methods
writeTSS	writeTSS-methods
writeTSS,tssObject,character,numeric,character,logical,character-method	writeTSS-methods
