axisTrack	axisTrack
Axt	Axt-class
Axt-class	Axt-class
axtChain	axtChain
axtInfo	axtInfo
binFromCoordRange	binner
binRangesFromCoordRange	binner
binRestrictionString	binner
blatCNE	blatCNE
c,Axt-method	Axt-class
c,GRangePairs-method	GRangePairs-class
ceScan	ceScan-methods
ceScan,Axt-method	ceScan-methods
ceScan,CNE-method	ceScan-methods
chainMergeSort	chainMergeSort
chainNetSyntenic	chainNetSyntenic
chainPreNet	chainPreNet
class:GRangePairs	GRangePairs-class
CNE	CNE-class
CNE-class	CNE-class
CNE12	CNE-class
CNE12,CNE-method	CNE-class
CNE21	CNE-class
CNE21,CNE-method	CNE-class
CNEDanRer10Hg38	CNEDanRer10Hg38
CNEDensity	CNEDensity
CNEDensity,ANY,character,character,missing,missing-method	CNEDensity
CNEDensity,ANY,missing,character,character,character-method	CNEDensity
CNEDensity-methods	CNEDensity
CNEFinal	CNE-class
CNEFinal,CNE-method	CNE-class
cneFinalListDanRer10Hg38	cneFinalListDanRer10Hg38
CNEHg38DanRer10	CNEDanRer10Hg38
cneMerge	cneMerge
cneMerge,CNE,missing-method	cneMerge
cneMerge,GRangePairs,GRangePairs-method	cneMerge
CNEMerged	CNE-class
CNEMerged,CNE-method	CNE-class
coerce,GRangePairs,GRanges-method	GRangePairs-class
coerce,GRangePairs,GRangesList-method	GRangePairs-class
cpgIslands	axisTrack
fetchChromSizes	fetchChromSizes
first,GRangePairs-method	GRangePairs-class
fixCoordinates	fixCoordinates
fixCoordinates,Axt-method	fixCoordinates
GRangePairs	GRangePairs-class
GRangePairs-class	GRangePairs-class
grangesPairsForDotplot	grangesPairsForDotplot
grglist,GRangePairs-method	GRangePairs-class
last	GRangePairs-class
last,GRangePairs-method	GRangePairs-class
lastal	last
lastz	lastz
lavToPsl	lavToPsl
length,Axt-method	Axt-class
makeAncoraFiles	makeAncoraFiles
makeCNEDensity	makeCNEDensity
makeGRBs	makeGRBs
matchDistribution	matchDistribution
matchDistribution,Axt-method	matchDistribution
N50	AssemblyStats
N90	AssemblyStats
netToAxt	netToAxt
orgKEGGIds2EntrezIDs	orgKEGGIds2EntrezIDs
plotCNEDistribution	plotCNEDistribution
plotCNEWidth	plotCNEWidth
psubAxt	psubAxt
queryCNEData	queryCNEData
queryRanges	Axt-class
queryRanges,Axt-method	Axt-class
querySeqs	Axt-class
querySeqs,Axt-method	Axt-class
read.rmMask.GRanges	read.rmMask.GRanges
read.rmskFasta	read.rmskFasta
readAncora	readAncora
readAncoraIntoSQLite	readAncoraIntoSQLite
readAxt	readAxt
readBed	readBed
readCNERangesFromSQLite	readCNERangesFromSQLite
refGenes	axisTrack
reverseCigar	reverseCigar
saveCNEToSQLite	saveCNEToSQLite
score,Axt-method	Axt-class
scoringMatrix	scoringMatrix
second,GRangePairs-method	GRangePairs-class
seqinfo,GRangePairs-method	GRangePairs-class
seqnames,GRangePairs-method	GRangePairs-class
strand,GRangePairs-method	GRangePairs-class
subAxt	subAxt-methods
subAxt,Axt,character,integer,integer-method	subAxt-methods
subAxt,Axt,character,missing,missing-method	subAxt-methods
subAxt,Axt,character,numeric,numeric-method	subAxt-methods
subAxt,Axt,GRanges,missing,missing-method	subAxt-methods
subAxt-methods	subAxt-methods
summary	Axt-util
summary,Axt-method	Axt-util
swap	GRangePairs-class
swap,GRangePairs-method	GRangePairs-class
symCount	Axt-class
symCount,Axt-method	Axt-class
syntenicDotplot	syntenicDotplot
syntenicDotplot,Axt-method	syntenicDotplot
syntenicDotplot,GRangePairs-method	syntenicDotplot
targetRanges	Axt-class
targetRanges,Axt-method	Axt-class
targetSeqs	Axt-class
targetSeqs,Axt-method	Axt-class
thresholds	CNE-class
thresholds,CNE-method	CNE-class
unique,GRangePairs-method	GRangePairs-class
unlist,GRangePairs-method	GRangePairs-class
writeAxt	writeAxt
[,Axt,ANY,ANY-method	Axt-class
