GAlignmentPairs-class   GAlignmentPairs objects
GAlignments-class       GAlignments objects
GAlignmentsList-class   GAlignmentsList objects
GappedReads-class       (Legacy) GappedReads objects
OverlapEncodings-class
                        OverlapEncodings objects
cigar-utils             CIGAR utility functions
coverage-methods        Coverage of a GAlignments, GAlignmentPairs, or
                        GAlignmentsList object
encodeOverlaps-methods
                        Encode the overlaps between RNA-seq reads and
                        the transcripts of a gene model
findCompatibleOverlaps-methods
                        Finding hits between reads and transcripts that
                        are _compatible_ with the splicing of the
                        transcript
findMateAlignment       Pairing the elements of a GAlignments object
findOverlaps-methods    Finding overlapping genomic alignments
findSpliceOverlaps-methods
                        Classify ranges (reads) as compatible with
                        existing genomic annotations or as having novel
                        splice events
intra-range-methods     Intra range transformations of a GAlignments or
                        GAlignmentsList object
junctions-methods       Extract junctions from genomic alignments
mapToAlignments         Map range coordinates between reads and genome
                        space using CIGAR alignments
pileLettersAt           Pile the letters of a set of aligned reads on
                        top of a set of genomic positions
readGAlignments         Reading genomic alignments from a file
sequenceLayer           Lay read sequences alongside the reference
                        space, using their CIGARs
setops-methods          Set operations on GAlignments objects
stackStringsFromBam     Stack the read sequences stored in a
                        GAlignments object or a BAM file
summarizeOverlaps-methods
                        Perform overlap queries between reads and
                        genomic features
