assembly1	CNE-class
assembly1,CNE-method	CNE-class
assembly2	CNE-class
assembly2,CNE-method	CNE-class
axisTrack	axisTrack
Axt	axt-class
Axt-class	axt-class
axtDanRer7Hg19	axtDanRer7Hg19
axtHg19DanRer7	axtDanRer7Hg19
axtInfo	axtInfo
binFromCoordRange	binner
binRangesFromCoordRange	binner
binRestrictionString	binner
blatCNE	blatCNE
c,Axt-method	axt-class
ceScan	ceScan-methods
ceScan,Axt,GRanges,GRanges,Seqinfo-method	ceScan-methods
ceScan,Axt,GRanges,missing,missing-method	ceScan-methods
ceScan,Axt,missing,GRanges,Seqinfo-method	ceScan-methods
ceScan,Axt,missing,missing,missing-method	ceScan-methods
ceScan,character,character,character,Seqinfo-method	ceScan-methods
ceScan,character,character,missing,missing-method	ceScan-methods
ceScan,character,missing,character,Seqinfo-method	ceScan-methods
ceScan,character,missing,missing,missing-method	ceScan-methods
ceScan-methods	ceScan-methods
ceScanOneStep	ceScanOneStep
CNE	CNE-class
CNE-class	CNE-class
CNE1	CNE-class
CNE1,CNE-method	CNE-class
CNE2	CNE-class
CNE2,CNE-method	CNE-class
cneBlatedDanRer7Hg19	cneBlatedDanRer7Hg19
CNEDanRer7Hg19	CNEHg19DanRer7
CNEDensity	CNEDensity
CNEDensity,ANY,character,character,missing,missing-method	CNEDensity
CNEDensity,ANY,missing,character,character,character-method	CNEDensity
CNEDensity-methods	CNEDensity
CNEHg19DanRer7	CNEHg19DanRer7
cneHg19DanRer7_45_50	cneHg19DanRer7_45_50
cneHg19DanRer7_48_50	cneHg19DanRer7_45_50
cneHg19DanRer7_49_50	cneHg19DanRer7_45_50
cneMerge	cneMerge
CNEMerged	CNE-class
CNEMerged,CNE-method	CNE-class
CNERepeatsFiltered	CNE-class
CNERepeatsFiltered,CNE-method	CNE-class
cpgIslands	axisTrack
fetchChromSizes	fetchChromSizes
finalCNE	finalCNE
ideoTrack	axisTrack
length,Axt-method	axt-class
nchar,Axt-method	axt-class
qSizesDanRer7	qSizesDanRer7
qSizesHg19	qSizesDanRer7
queryCNEData	queryCNEData
queryRanges	axt-class
queryRanges,Axt-method	axt-class
querySeqs	axt-class
querySeqs,Axt-method	axt-class
readAxt	readAxt
readBed	readBed
readCNERangesFromSQLite	readCNERangesFromSQLite
refGenes	axisTrack
reverseCigar	reverseCigar
saveCNEToSQLite	saveCNEToSQLite
saveCNEToSQLite,CNE,ANY,missing-method	saveCNEToSQLite
saveCNEToSQLite,data.frame,ANY,character-method	saveCNEToSQLite
saveCNEToSQLite-methods	saveCNEToSQLite
score,Axt-method	axt-class
subAxt	subAxt-methods
subAxt,Axt,character,missing,missing-method	subAxt-methods
subAxt,Axt,character,numeric,numeric-method	subAxt-methods
subAxt-methods	subAxt-methods
symCount	axt-class
symCount,Axt-method	axt-class
targetRanges	axt-class
targetRanges,Axt-method	axt-class
targetSeqs	axt-class
targetSeqs,Axt-method	axt-class
thresholds	CNE-class
thresholds,CNE-method	CNE-class
writeAxt	writeAxt
[,Axt,ANY,ANY-method	axt-class
