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| annotateNearest | Annotate Nearest |
| boundedClusterMaker | Make clusters of genomic locations based on distance |
| bumphunter | Bumphunter |
| bumphunter-method | Bumphunter |
| bumphunter-methods | Bumphunter |
| bumphunterEngine | Bumphunter |
| clusterMaker | Make clusters of genomic locations based on distance |
| dummyData | Generate dummy data for use with bumphunter functions |
| getSegments | Segment a vector into positive, zero, and negative regions |
| locfitByCluster | Apply local regression smoothing to values within each spatially-defined cluster. |
| loessByCluster | Apply loess smoothing to values within each spatially-defined cluster. |
| matchGenes | Annotate Nearest |
| pointMatch | Fuzzy Matching of Genomic Locations |
| print.bumps | Bumphunter |
| regionFinder | Find non-zero regions in vector |
| regionMatch | Annotate Nearest |
| runmedByCluster | Apply running median smoothing to values within each spatially-defined cluster |
| smoother | Smooth genomic profiles |
| TT | HG19 Transcripts |