| 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"' |