Man pages for GenomicAlignments
Representation and manipulation of short genomic alignments
| cigar-utils | CIGAR utility functions |
| coordinate-mapping-methods | Map range coordinates between reads and genome space using... |
| coverage-methods | Coverage of a GAlignments, GAlignmentPairs, or... |
| encodeOverlaps-methods | Encode the overlaps between RNA-seq reads and the transcripts... |
| findCompatibleOverlaps-methods | Finding hits between reads and transcripts that are... |
| findMateAlignment | Pairing the elements of a GAlignments object |
| findOverlaps-methods | Finding overlapping genomic alignments |
| findSpliceOverlaps-methods | Classify ranges (reads) as compatible with existing genomic... |
| GAlignmentPairs-class | GAlignmentPairs objects |
| GAlignments-class | GAlignments objects |
| GAlignmentsList-class | GAlignmentsList objects |
| GappedReads-class | (Legacy) GappedReads objects |
| intra-range-methods | Intra range transformations of a GAlignments or... |
| junctions-methods | Extract junctions from genomic alignments |
| OverlapEncodings-class | OverlapEncodings objects |
| pileLettersAt | Pile the letters of a set of aligned reads on top of a set of... |
| readGAlignments | Reading genomic alignments from a file |
| sequenceLayer | Lay read sequences alongside the reference space, using their... |
| setops-methods | Set operations on GAlignments objects |
| stackStringsFromGAlignments | Stack the read sequences stored in a GAlignments object or a... |
| summarizeOverlaps-methods | Perform overlap queries between reads and genomic features |
