activeChrs	activeChrs
annotateTSS	annotateTSS
CapSet	newCapSet
CapSet-class	newCapSet
check_capSet	check_capSet
demultiplexFASTQ	demultiplexFASTQ
demultiplexFASTQ,CapSet-method	demultiplexFASTQ
detectDiffTSS	detectDiffTSS
detectDiffTSS,DESeqDataSet-method	detectDiffTSS
detectDiffTSS,DGEGLM-method	detectDiffTSS
detectTSS	detectTSS
detectTSS,CapSet-method	detectTSS
diffQCplots	diffQCplots
exampleCSobject	exampleCSobject
exportTSS	exportTSS
exportTSS,CapSet-method	exportTSS
filterDuplicates	filterDuplicates
filterDuplicates,CapSet-method	filterDuplicates
filterDups	filterDups
fitDiffTSS	fitDiffTSS
fitDiffTSS,CapSet-method	fitDiffTSS
getBamFlags	getBamFlags
getChromBins	getChromBins
getChromWindows	getChromWindows
getGeneCounts	getGeneCounts
getGeneCounts,CapSet-method	getGeneCounts
getMCparams	getMCparams
getNormFactors	getNormFactors
getNormFactors,CapSet-method	getNormFactors
getranks	getranks
get_newfastq	get_newfastq
mapCaps	mapCaps
mapCaps,CapSet-method	mapCaps
newCapSet	newCapSet
numReadsInBed	numReadsInBed
plotPrecision	plotPrecision
plotReadStats	plotReadStats
plotReadStats,CapSet-method	plotReadStats
plotTSSprecision	plotTSSprecision
plotTSSprecision,GRanges,CapSet-method	plotTSSprecision
plotTSSprecision,GRanges,character-method	plotTSSprecision
readsTo3p	readsTo3p
readsTo5p	readsTo5p
readsToCenter	readsToCenter
sampleInfo	sampleInfo
sampleInfo,CapSet-method	sampleInfo
sampleInfo<-	sampleInfo
sampleInfo<-,CapSet-method	sampleInfo
splitBAM_byIndex	splitBAM_byIndex
splitBAM_byRepindex	splitBAM_byRepindex
splitranks	splitranks
split_fastq	split_fastq
strandBinCounts	strandBinCounts
