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GenomicAlignments (version 1.8.4)

Representation and manipulation of short genomic alignments

Description

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

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Version

Version

1.8.4

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in GenomicAlignments (1.8.4)

intra-range-methods

Intra range transformations of a GAlignments or GAlignmentsList object

GAlignmentPairs-class

GAlignmentPairs objects

GAlignments-class

GAlignments objects

summarizeOverlaps-methods

Perform overlap queries between reads and genomic features

junctions-methods

Extract junctions from genomic alignments

coverage-methods

Coverage of a GAlignments, GAlignmentPairs, or GAlignmentsList object

encodeOverlaps-methods

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

OverlapEncodings-class

OverlapEncodings objects

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

findOverlaps-methods

Finding overlapping genomic alignments

findSpliceOverlaps-methods

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

GAlignmentsList-class

GAlignmentsList objects

GappedReads-class

(Legacy) GappedReads objects

findCompatibleOverlaps-methods

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

CIGAR utility functions

mapToAlignments

Map range coordinates between reads and genome space using CIGAR alignments

readGAlignments

Reading genomic alignments from a file

Lay read sequences alongside the reference space, using their CIGARs

findMateAlignment

Pairing the elements of a GAlignments object

Set operations on GAlignments objects

stackStringsFromBam

Stack the read sequences stored in a BAM file on a region of interest