GRanges-class           GRanges objects
GRanges-setops          GRanges and GRangesList Set and Parallel Set
                        Operations
GRangesList-class       GRangesList objects
GappedAlignments-class
                        GappedAlignments objects
GenomicRanges-comparison
                        Ordering and comparing genomic ranges
Seqinfo-class           Seqinfo objects
SummarizedExperiment-class
                        SummarizedExperiment instances
cigar-utils             CIGAR utility functions
countGenomicOverlaps    Count Read Hits in Genomic Features
findOverlaps,GenomicRanges,GenomicRanges-method
                        GRanges and GRangesList Interval Overlaps
seqinfo                 Accessing sequence information
strand                  Accessing strand information
