GenomicAlignments

GAlignmentPairs objects

GAlignments objects

GAlignmentsList objects

(Legacy) GappedReads objects

OverlapEncodings objects

CIGAR utility functions

Map range coordinates between reads and genome space using CIGAR alignments

Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList object

Encode the overlaps between RNA-seq reads and the transcripts of a gene model

Finding hits between reads and transcripts that are compatible with the splicing of the transcript

Pairing the elements of a GAlignments object

Finding overlapping genomic alignments

Classify ranges (reads) as compatible with existing genomic annotations or as having novel splice events

Intra range transformations of a GAlignments or GAlignmentsList object

Extract junctions from genomic alignments

Pile the letters of a set of aligned reads on top of a set of genomic positions

Reading genomic alignments from a file

Lay read sequences alongside the reference space, using their CIGARs

Set operations on GAlignments objects

Stack the read sequences stored in a GAlignments object or a BAM file

Perform overlap queries between reads and genomic features