| BinBam | BinBam |
| createReferenceSetFromCounts | createReferenceSetFromCounts |
| evalPerformance | evalPerformance |
| gcContent | gcContent in 20kb bins |
| makeBinnedCountsFile | makeBinnedCountsFile |
| makeGCContentData | makeGCContentData |
| makeGCContentPerPos | makeGCContentPerPos |
| outcomes | set of simulated outcomes data |
| plotTestSample | plotTestSample |
| print.rapidr.ref | print.rapidr.ref |
| print.rapidr.test | print.rapidr.test |
| ReadBed | ReadBed |
| testUnknowns | testUnknowns |
| writeCleanedCountsFile | writeCleanedCountsFiles |
| writeResultsToFile | writeResultsToFile |