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
OrientationFrame Man page Source code
OrientationFrame-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
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
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,OrientationFrame,ContigOrdering-method Man page
writeBed-OrientationFrame-ContigOrdering-method Man page
writeBed.func Source code
contiBAIT documentation built on Nov. 17, 2017, 2:06 p.m.