| alignmentStats | Get statistics on alignments |
| preprocessReads | Preprocess Short Reads |
| qAlign | Align reads |
| qCount | Quantify alignments |
| qExportWig | QuasR wig file export |
| qMeth | Quantify DNA methylation |
| qProfile | Quantify alignments by relative position |
| qProject-class | qProject objects |
| qProjectUpdate | Update qProject |
| qQCReport | QuasR Quality Control Report |
| QuasR-package | Quantify and Annotate Short Reads in R |
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