API for contiBAIT
Improves Early Build Genome Assemblies using Strand-Seq Data

Global functions
BAIT	Man page Source code
ChrTable	Man page Source code
ChrTable-class	Man page
ContigOrdering	Man page Source code
ContigOrdering-class	Man page
LibraryGroupList	Man page Source code
LibraryGroupList-class	Man page
LinkageGroupList	Man page Source code
LinkageGroupList-class	Man page
StrandFreqMatrix	Man page Source code
StrandFreqMatrix-class	Man page
StrandReadMatrix	Man page Source code
StrandReadMatrix-class	Man page
StrandStateList	Man page Source code
StrandStateList-class	Man page
StrandStateMatrix	Man page Source code
StrandStateMatrix-class	Man page
StrandStateMatrixValidity	Source code
barplotLinkageGroupCalls	Man page
barplotLinkageGroupCalls,LinkageGroupList,ChrTable-method	Man page
barplotLinkageGroupCalls,LinkageGroupList,LinkageGroupList-metho	Man page
barplotLinkageGroupCalls.func	Source code
clusterContigs	Man page
clusterContigs,StrandStateMatrix,StrandStateMatrix-method	Man page
clusterContigs,StrandStateMatrix-method	Man page
clusterContigs.func	Source code
computeConsensus	Source code
computeSim	Source code
contiBAIT	Man page Source code
exampleChrTable	Man page
exampleContigOrder	Man page
exampleCrickFreq	Man page
exampleDividedChr	Man page
exampleLGList	Man page
exampleLibList	Man page
exampleReadCounts	Man page
exampleStrandFreq	Man page
exampleWCMatrix	Man page
exampleWatsonFreq	Man page
findSexGroups	Man page
findSexGroups,LinkageGroupList,StrandStateMatrix-method	Man page
findSexGroups.func	Source code
findSimilarLibraries	Man page
findSimilarLibraries,StrandStateMatrix,StrandReadMatrix,ChrTable	Man page
findSimilarLibraries,findSimilarLibraries-StrandStateMatrix-Stra	Man page
findSimilarLibraries.func	Source code
fixLinkageGroups	Man page
fixLinkageGroups,ContigOrdering,StrandStateList,LinkageGroupList	Man page
fixLinkageGroups-ContigOrdering-StrandStateList-method	Man page
fixLinkageGroups.func	Source code
flipOrderedLinkageGroups	Man page
flipOrderedLinkageGroups,ContigOrdering,StrandStateList,LinkageG	Man page
flipOrderedLinkageGroups-ContigOrdering-StrandStateList-method	Man page
flipOrderedLinkageGroups.func	Source code
highlightAssemblyErrors	Man page Source code
highlightAssemblyErrors,highlightAssemblyErrors-GRanges-method	Man page
ideogramPlot	Man page
ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method	Man page
ideogramPlot,StrandReadMatrix,StrandReadMatrix-method,ChrTable,C	Man page
ideogramPlot.func	Source code
locateMisorients	Man page
locateMisorients,GRanges-method	Man page
locateMisorients,locateMisorients-GRanges-method	Man page
locateMisorients.func	Source code
makeBoxPlot	Man page
makeBoxPlot,ChrTable,LinkageGroupList-method	Man page
makeBoxPlot-ChrTable-LinkageGroupList-method	Man page
makeBoxPlot.func	Source code
makeChrTable	Man page Source code
mapGapFromOverlap	Man page Source code
mergeFlankedLGs	Man page
mergeFlankedLGs,LinkageGroupList,StrandStateMatrix-method	Man page
mergeFlankedLGs.func	Source code
orderAllLinkageGroups	Man page
orderAllLinkageGroups,LinkageGroupList,StrandStateMatrix,StrandF	Man page
orderAllLinkageGroups,orderAllLinkageGroups-LinkageGroupList-Str	Man page
orderAllLinkageGroups.func	Source code
orderContigsGreedy	Man page Source code
orderContigsTSP	Man page Source code
plotContigOrder	Man page
plotContigOrder,ContigOrdering-method	Man page
plotContigOrder.func	Source code
plotLGDistances	Man page
plotLGDistances,LinkageGroupList,LinkageGroupList-method	Man page
plotLGDistances,LinkageGroupList,StrandStateMatrix-method	Man page
plotLGDistances.func	Source code
plotWCdistribution	Man page
plotWCdistribution,StrandFreqMatrix,StrandFreqMatrix-method	Man page
plotWCdistribution,StrandFreqMatrix-method	Man page
plotWCdistribution.func	Source code
preprocessStrandTable	Man page
preprocessStrandTable,StrandFreqMatrix,StrandFreqMatrix-method	Man page
preprocessStrandTable,StrandFreqMatrix-method	Man page
preprocessStrandTable.func	Source code
reorientAndMergeLGs	Man page
reorientAndMergeLGs,LinkageGroupList,StrandStateMatrix-method	Man page
reorientAndMergeLGs-LinkageGroupList-StrandStateMatrix-method	Man page
reorientAndMergeLGs.func	Source code
show,ContigOrdering-method	Man page
show,LibraryGroupList-method	Man page
show,LinkageGroupList-method	Man page
show,OrientationFrame-method	Man page
show,StrandFreqMatrix-method	Man page
show,StrandReadMatrix-method	Man page
show,StrandStateList-method	Man page
show,StrandStateMatrix-method	Man page
strandSeqFreqTable	Man page Source code
thoroughBed	Man page
thoroughBed,ANY,LibraryGroupList-method	Man page
thoroughBed,thoroughBed-LibraryGroupList-method	Man page
thoroughBed.func	Source code
writeBed	Man page
writeBed,ANY,ChrTable,ContigOrdering-method	Man page
writeBed-ChrTable-ContigOrdering-method	Man page
writeBed.func	Source code