| anno_rCRS | annotation for the regions (genic and not) of the rCRS... |
| byStrand | simple helper function to split a *RangesList by the strand... |
| callMT | call mitochondrial variants against rCRS from an... |
| chrominfo.rCRS | Sequence information (seqinfo) for the rCRS mitogenome |
| filterMT | Filter SummarizedExperiment or DataFrame values based on its... |
| filterMTvars | sanitize PASSing mitochondrial variant calls to a moderate... |
| fixMetadata | fix metadata for an MAlignmentsList or MVRangesList, if... |
| fpFilter_RSRS | false positive filter (fpFilter) for RSRS... |
| fpFilter_Triska | a false positive (fp) filter from Petr Triska's manuscript on... |
| getMT | grab the mitochondrial reads from a BAM & estimate their... |
| hg19TorCRS | a liftOver chain for hg19 to rCRS attempts. We do not... |
| indexMTGenome | build and install GmapGenome.[organism].[mtGenome], currently... |
| injectMTVariants | Inject (one or more) variants against rCRS. |
| MAlignments-class | wraps a GAlignments with information about coverage and its... |
| MAlignmentsList-class | wraps a GAlignmentsList (made up of MAlignments) for nicer... |
| MAlignmentsList-methods | wrap a GAlignmentsList for viewing |
| MAlignments-methods | wrap a GAlignments for easier stats |
| mtAnno | annotation for the rCRS genome |
| MTcircos | plot a canonical human (or, in principle, any) mitochondrial... |
| MTcomplex | plot the (putative) functional impact of mutations to ETP... |
| MTcoverage | Mitochondrial genome coverage and plots for MAlignments or... |
| mtGenes | Base sequences of mitochondrial coding genes. |
| mtGenes.rCRS | All annotated gene regions (not just coding genes) from rCRS. |
| MTHGVS | convert mitochondrial variant calls to HGVS format for naming |
| MVRanges-class | like a VRanges, but for mitochondria |
| MVRangesList-class | like a VRangesList, but for mitochondria |
| MVRangesList-methods | Wrap a VRangesList for mitochondrial use. |
| MVRanges-methods | wrap a VRanges for mitochondrial use |
| rCRSeq | The complete sequence of the human rCRS mitogenome. Yes, it's... |
| s4Methods | List all defined methods for an S4 class (or classes, if you... |
| validMetadata | Ensure that the metadata caches in MAlignmentsLists and... |
