Constraints             Enforcing constraints thru Constraint objects
GRanges-class           GRanges objects
GRangesList-class       GRangesList objects
GappedAlignmentPairs-class
                        GappedAlignmentPairs objects
GappedAlignments-class
                        GappedAlignments objects
GenomicRanges-comparison
                        Comparing and ordering 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        Coverage of a GRanges, GRangesList,
                        GappedAlignments, or GappedAlignmentPairs
                        object
encodeOverlaps-methods
                        encodeOverlaps methods and related utilities
findOverlaps-methods    GRanges, GRangesList, GappedAlignments and
                        GappedAlignmentPairs Interval Overlaps
keepSeqlevels           seqlevels utility functions
map,GenomicRanges,GRangesList-method
                        Mapping ranges between sequences
seqinfo                 Accessing sequence information
setops-methods          Set operations on
                        GRanges/GRangesList/GappedAlignments objects
strand-utils            Strand utilities
summarizeOverlaps       Count reads that map to genomic features
