GRanges-class           GRanges objects
GRangesList-class       GRangesList objects
GappedAlignments-class
                        GappedAlignments objects
GenomicRanges-comparison
                        Ordering and comparing genomic ranges
GenomicRangesList-class
                        GenomicRangesList objects
Seqinfo-class           Seqinfo objects
SummarizedExperiment-class
                        SummarizedExperiment instances
cigar-utils             CIGAR utility functions
countGenomicOverlaps    Count Read Hits in Genomic Features
coverage-methods        GRanges, GRangesList and GappedAlignments
                        coverage
findOverlaps-methods    GRanges, GRangesList and GappedAlignments
                        Interval Overlaps
keepSeqlevels           seqlevels utility functions
seqinfo                 Accessing sequence information
setops-methods          Set operations on
                        GRanges/GRangesList/GappedAlignments objects
strand                  Accessing strand information
summarizeOverlaps       Count reads that map to genomic features
