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 method for GRangesList objects,
                        and related utilities
findOverlaps-methods    GRanges, GRangesList, GappedAlignments and
                        GappedAlignmentPairs Interval Overlaps
findSpliceOverlaps      Classify ranges (reads) as compatible with
                        existing genomic annotations or as having novel
                        splice events
inter-range-methods     Inter range transformations of a GenomicRanges
                        object
intra-range-methods     Intra range transformations of a GenomicRanges
                        object
keepSeqlevels           seqlevels utility functions
map,GenomicRanges,GRangesList-method
                        Mapping ranges between sequences
nearest-methods         Finding the nearest genomic range neighbor
phicoef                 Calculate the "phi coefficient" between two
                        binary variables
seqinfo                 Accessing sequence information
setops-methods          Set operations on
                        GRanges/GRangesList/GappedAlignments objects
strand-utils            Strand utilities
summarizeOverlaps       Perform overlap queries between reads and
                        genomic features
