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