# Recovering Structure of Long Molecules from Structural Variation Data

## Documentation for package ‘SVAlignR’ version 0.9.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

alignAllClusters | Class '"AlignedCluster"'
alignCluster | Class '"AlignedCluster"'
AlignedCluster-class | Class '"AlignedCluster"'
Breakpoints | Class '"Breakpoints"'
breakpoints | SVAlignR Sample Data
Breakpoints-class | Class '"Breakpoints"'
Cipher | Class '"Cipher"'
Cipher-class | Class '"Cipher"'
countWords | Class '"Words"'
deBruijn | Class '"DeBruijn"'
DeBruijn-class | Class '"DeBruijn"'
decode | Class '"Cipher"'
DecompositionGraph | Class '"StringGraph"'
encode | Class '"Cipher"'
exportSG | Class '"StringGraph"'
heat | Class '"SequenceCluster"'
image-method | Class '"AlignedCluster"'
longreads | SVAlignR Sample Data
makeSubsMatrix | Class '"AlignedCluster"'
makeWords | Class '"Words"'
MotifGraph | Class '"StringGraph"'
plot-method | Class '"SequenceCluster"'
plot-method | Class '"StringGraph"'
plot-method | Class '"Breakpoints"'
plotWords | Class '"Words"'
SequenceCluster | Class '"SequenceCluster"'
SequenceCluster-class | Class '"SequenceCluster"'
StringGraph | Class '"StringGraph"'
StringGraph-class | Class '"StringGraph"'
SVAlignR-data | SVAlignR Sample Data
updateClusters | Class '"SequenceCluster"'