alignAllClusters	03-align
alignCluster	03-align
AlignedCluster-class	03-align
Breakpoints	07-breakpoints
breakpoints	00-datasets
Breakpoints-class	07-breakpoints
Cipher	01-cipher
Cipher-class	01-cipher
countWords	06-words
deBruijn	08-debruijn
DeBruijn-class	08-debruijn
decode	01-cipher
DecompositionGraph	05-stringGraph
encode	01-cipher
exportSG	05-stringGraph
getEvidence	09-evidence
heat	02-seqclust
image,AlignedCluster-method	03-align
longreads	00-datasets
makeSubsMatrix	03-align
makeWords	06-words
MotifGraph	05-stringGraph
plot,Breakpoints,missing-method	07-breakpoints
plot,SequenceCluster,missing-method	02-seqclust
plot,StringGraph,ANY-method	05-stringGraph
plotWords	06-words
SequenceCluster	02-seqclust
SequenceCluster-class	02-seqclust
showCoverage	09-evidence
StringGraph	05-stringGraph
StringGraph-class	05-stringGraph
SVAlignR-data	00-datasets
updateClusters	02-seqclust
