BAIT	BAIT
barplotLinkageGroupCalls	barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
barplotLinkageGroupCalls,LinkageGroupList,ChrTable-method	barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
barplotLinkageGroupCalls,LinkageGroupList,LinkageGroupList-method,ChrTable,ChrTable-method	barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
ChrTable	ChrTable
ChrTable-class	ChrTable
clusterContigs	clusterContigs-StrandStateMatrix-method
clusterContigs,StrandStateMatrix,StrandStateMatrix-method	clusterContigs-StrandStateMatrix-method
clusterContigs,StrandStateMatrix-method	clusterContigs-StrandStateMatrix-method
contiBAIT	contiBAIT
ContigOrdering	ContigOrdering
ContigOrdering-class	ContigOrdering
exampleChrTable	exampleChrTable
exampleContigOrder	exampleContigOrder
exampleCrickFreq	exampleCrickFreq
exampleDividedChr	exampleDividedChr
exampleLGList	exampleLGList
exampleLibList	exampleLibList
exampleReadCounts	exampleReadCounts
exampleStrandFreq	exampleStrandFreq
exampleWatsonFreq	exampleWatsonFreq
exampleWCMatrix	exampleWCMatrix
findSexGroups	findSexGroups-LinkageGroupList-StrandStateMatrix-method
findSexGroups,LinkageGroupList,StrandStateMatrix-method	findSexGroups-LinkageGroupList-StrandStateMatrix-method
findSimilarLibraries	findSimilarLibraries
findSimilarLibraries,findSimilarLibraries-StrandStateMatrix-StrandReadMatrix-ChrTable-method	findSimilarLibraries
findSimilarLibraries,StrandStateMatrix,StrandReadMatrix,ChrTable-method	findSimilarLibraries
fixLinkageGroups	fixLinkageGroups
fixLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList-method	fixLinkageGroups
fixLinkageGroups-ContigOrdering-StrandStateList-method	fixLinkageGroups
flipOrderedLinkageGroups	flipOrderedLinkageGroups
flipOrderedLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList,StrandStateMatrix-method	flipOrderedLinkageGroups
flipOrderedLinkageGroups-ContigOrdering-StrandStateList-method	flipOrderedLinkageGroups
highlightAssemblyErrors	highlightAssemblyErrors
highlightAssemblyErrors,highlightAssemblyErrors-GRanges-method	highlightAssemblyErrors
ideogramPlot	ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method	ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
ideogramPlot,StrandReadMatrix,StrandReadMatrix-method,ChrTable,ChrTable-method	ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
LibraryGroupList	LibraryGroupList
LibraryGroupList-class	LibraryGroupList
LinkageGroupList	LinkageGroupList
LinkageGroupList-class	LinkageGroupList
locateMisorients	locateMisorients
locateMisorients,GRanges-method	locateMisorients
locateMisorients,locateMisorients-GRanges-method	locateMisorients
makeBoxPlot	makeBoxPlot
makeBoxPlot,ChrTable,LinkageGroupList-method	makeBoxPlot
makeBoxPlot-ChrTable-LinkageGroupList-method	makeBoxPlot
makeChrTable	makeChrTable
mapGapFromOverlap	mapGapFromOverlap
mergeFlankedLGs	mergeFlankedLGs
mergeFlankedLGs,LinkageGroupList,StrandStateMatrix-method	mergeFlankedLGs
orderAllLinkageGroups	orderAllLinkageGroups
orderAllLinkageGroups,LinkageGroupList,StrandStateMatrix,StrandFreqMatrix,StrandReadMatrix-method	orderAllLinkageGroups
orderAllLinkageGroups,orderAllLinkageGroups-LinkageGroupList-StrandStateMatrix-StrandFreqMatrix-StrandReadMatrix-method	orderAllLinkageGroups
orderContigsGreedy	orderContigsGreedy
orderContigsTSP	orderContigsTSP
plotContigOrder	plotContigOrder
plotContigOrder,ContigOrdering-method	plotContigOrder
plotLGDistances	plotLGDistances-LinkageGroupList-StrandStateMatrix-method
plotLGDistances,LinkageGroupList,LinkageGroupList-method	plotLGDistances-LinkageGroupList-StrandStateMatrix-method
plotLGDistances,LinkageGroupList,StrandStateMatrix-method	plotLGDistances-LinkageGroupList-StrandStateMatrix-method
plotWCdistribution	plotWCdistribution-StrandFreqMatrix-method
plotWCdistribution,StrandFreqMatrix,StrandFreqMatrix-method	plotWCdistribution-StrandFreqMatrix-method
plotWCdistribution,StrandFreqMatrix-method	plotWCdistribution-StrandFreqMatrix-method
preprocessStrandTable	preprocessStrandTable-StrandFreqMatrix-method
preprocessStrandTable,StrandFreqMatrix,StrandFreqMatrix-method	preprocessStrandTable-StrandFreqMatrix-method
preprocessStrandTable,StrandFreqMatrix-method	preprocessStrandTable-StrandFreqMatrix-method
reorientAndMergeLGs	reorientAndMergeLGs
reorientAndMergeLGs,LinkageGroupList,StrandStateMatrix-method	reorientAndMergeLGs
reorientAndMergeLGs-LinkageGroupList-StrandStateMatrix-method	reorientAndMergeLGs
show,ContigOrdering-method	show-ContigOrdering-method
show,LibraryGroupList-method	show-LibraryGroupList-method
show,LinkageGroupList-method	show-LinkageGroupList-method
show,OrientationFrame-method	show-OrientationFrame-method
show,StrandFreqMatrix-method	show-StrandFreqMatrix-method
show,StrandReadMatrix-method	show-StrandReadMatrix-method
show,StrandStateList-method	show-StrandStateList-method
show,StrandStateMatrix-method	show-StrandStateMatrix-method
StrandFreqMatrix	StrandFreqMatrix
StrandFreqMatrix-class	StrandFreqMatrix
StrandReadMatrix	StrandReadMatrix
StrandReadMatrix-class	StrandReadMatrix
strandSeqFreqTable	strandSeqFreqTable
StrandStateList	StrandStateList
StrandStateList-class	StrandStateList
StrandStateMatrix	StrandStateMatrix
StrandStateMatrix-class	StrandStateMatrix
thoroughBed	thoroughBed
thoroughBed,ANY,LibraryGroupList-method	thoroughBed
thoroughBed,thoroughBed-LibraryGroupList-method	thoroughBed
writeBed	writeBed
writeBed,ANY,ChrTable,ContigOrdering-method	writeBed
writeBed-ChrTable-ContigOrdering-method	writeBed
