Man pages for Bioconductor-mirror/GenomicAlignments
Representation and manipulation of short genomic alignments

cigar-utilsCIGAR utility functions
coordinate-mapping-methodsMap range coordinates between reads and genome space using...
coverage-methodsCoverage of a GAlignments, GAlignmentPairs, or...
encodeOverlaps-methodsEncode the overlaps between RNA-seq reads and the transcripts...
findCompatibleOverlaps-methodsFinding hits between reads and transcripts that are...
findMateAlignmentPairing the elements of a GAlignments object
findOverlaps-methodsFinding overlapping genomic alignments
findSpliceOverlaps-methodsClassify ranges (reads) as compatible with existing genomic...
GAlignmentPairs-classGAlignmentPairs objects
GAlignments-classGAlignments objects
GAlignmentsList-classGAlignmentsList objects
GappedReads-class(Legacy) GappedReads objects
intra-range-methodsIntra range transformations of a GAlignments or...
junctions-methodsExtract junctions from genomic alignments
OverlapEncodings-classOverlapEncodings objects
pileLettersAtPile the letters of a set of aligned reads on top of a set of...
readGAlignmentsReading genomic alignments from a file
sequenceLayerLay read sequences alongside the reference space, using their...
setops-methodsSet operations on GAlignments objects
stackStringsFromBamStack the read sequences stored in a BAM file on a region of...
summarizeOverlaps-methodsPerform overlap queries between reads and genomic features
Bioconductor-mirror/GenomicAlignments documentation built on Aug. 17, 2017, 3:44 p.m.