esATAC-package	esATAC-package
atacBam2Bed	BamToBed
atacBam2Bed,ATACProc-method	BamToBed
atacBamSort	Rsortbam
atacBamSort,ATACProc-method	Rsortbam
atacBedToBigWig	BedToBigWig
atacBedToBigWig,ATACProc-method	BedToBigWig
atacBedUtils	BedUtils
atacBedUtils,ATACProc-method	BedUtils
atacBowtie2Mapping	Bowtie2Mapping
atacBowtie2Mapping,ATACProc-method	Bowtie2Mapping
atacCutSiteCount	CutSiteCountR
atacCutSiteCount,ATACProc-method	CutSiteCountR
atacExtractCutSite	CutSitePre
atacExtractCutSite,ATACProc-method	CutSitePre
atacFragLenDistr	FragLenDistr
atacFragLenDistr,ATACProc-method	FragLenDistr
atacFripQC	FripQC
atacFripQC,ATACProc-method	FripQC
atacGOAnalysis	RGo
atacGOAnalysis,ATACProc-method	RGo
atacLibComplexQC	LibComplexQC
atacLibComplexQC,ATACProc-method	LibComplexQC
atacMotifScan	RMotifScan
atacMotifScan,ATACProc-method	RMotifScan
atacMotifScanPair	RMotifScanPair
atacMotifScanPair,ATACProc-method	RMotifScanPair
atacPeakAnno	RPeakAnno
atacPeakAnno,ATACProc-method	RPeakAnno
atacPeakCalling	PeakCallingFseq
atacPeakCalling,ATACProc-method	PeakCallingFseq
atacpeakComp	RPeakComp
atacpeakComp,ATACProc-method	RPeakComp
atacPeakQC	PeakQC
atacPeakQC,ATACProc-method	PeakQC
atacPipe	esATAC-package
atacPipe2	atacPipe2
atacPrintMap	ATACProc-class
atacPrintMap,ATACProc-method	ATACProc-class
ATACProc-class	ATACProc-class
atacQCReport	FastQC
atacQCReport,ATACProc-method	FastQC
atacRemoveAdapter	RemoveAdapter
atacRemoveAdapter,ATACProc-method	RemoveAdapter
atacRenamer	Renamer
atacRenamer,ATACProc-method	Renamer
atacRepsPipe	atacRepsPipe
atacRepsPipe2	atacRepsPipe2
atacSam2Bam	SamToBam
atacSam2Bam,ATACProc-method	SamToBam
atacSamToBed	SamToBed
atacSamToBed,ATACProc-method	SamToBed
atacSNPAnno	RSNPs
atacSNPAnno,ATACProc-method	RSNPs
atacTSSQC	TSSQC
atacTSSQC,ATACProc-method	TSSQC
atacUnzipAndMerge	UnzipAndMerge
bam2bed	BamToBed
bamsort	Rsortbam
BamToBed	BamToBed
BedToBigWig	BedToBigWig
bedToBigWig	BedToBigWig
BedUtils	BedUtils
bedUtils	BedUtils
Bowtie2Mapping	Bowtie2Mapping
bowtie2Mapping	Bowtie2Mapping
clearProcCache	ATACProc-class
clearProcCache,ATACProc-method	ATACProc-class
configureValue	configureValue
cutsitecount	CutSiteCountR
CutSiteCountR	CutSiteCountR
CutSitePre	CutSitePre
extractcutsite	CutSitePre
FastQC	FastQC
FragLenDistr	FragLenDistr
fragLenDistr	FragLenDistr
FRiPQC	FripQC
fripQC	FripQC
getAllConfigure	configureValue
getConfigure	configureValue
getMotifPWM	getMotifPWM
getParam	ATACProc-class
getParam,ATACProc-method	ATACProc-class
getParamItems	ATACProc-class
getParamItems,ATACProc-method	ATACProc-class
getProcName	ATACProc-class
getProcName,ATACProc-method	ATACProc-class
getReportItems	ATACProc-class
getReportItems,ATACProc-method	ATACProc-class
getReportVal	ATACProc-class
getReportVal,ATACProc-method	ATACProc-class
goanalysis	RGo
isReady	ATACProc-class
isReady,ATACProc-method	ATACProc-class
isSingleEnd	ATACProc-class
isSingleEnd,ATACProc-method	ATACProc-class
LibComplexQC	LibComplexQC
libComplexQC	LibComplexQC
motifscan	RMotifScan
motifscanpair	RMotifScanPair
peakanno	RPeakAnno
peakCalling	PeakCallingFseq
PeakCallingFseq	PeakCallingFseq
peakcomp	RPeakComp
PeakQC	PeakQC
peakQC	PeakQC
printMap	ATACProc-class
process	ATACProc-class
process,ATACProc-method	ATACProc-class
qcreport	FastQC
RemoveAdapter	RemoveAdapter
removeAdapter	RemoveAdapter
Renamer	Renamer
renamer	Renamer
RGo	RGo
RMotifScan	RMotifScan
RMotifScanPair	RMotifScanPair
RPeakAnno	RPeakAnno
RPeakComp	RPeakComp
RSNPs	RSNPs
Rsortbam	Rsortbam
sam2bam	SamToBam
SamToBam	SamToBam
SamToBed	SamToBed
samToBed	SamToBed
scanGenomeMotif	scanGenomeMotif
setConfigure	configureValue
snpanno	RSNPs
TSSQC	TSSQC
tssQC	TSSQC
UnzipAndMerge	UnzipAndMerge
unzipAndMerge	UnzipAndMerge
