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GenomicAlignments (version 1.6.1)

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

1.6.1

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in GenomicAlignments (1.6.1)

findCompatibleOverlaps-methods

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

Pairing the elements of a GAlignments object
findOverlaps-methods

Finding overlapping genomic alignments
findSpliceOverlaps-methods

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

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

Reading genomic alignments from a file
GAlignmentsList-class

GAlignmentsList objects
GappedReads-class

(Legacy) GappedReads objects
GAlignmentPairs-class

GAlignmentPairs objects
GAlignments-class

GAlignments objects
sequenceLayer

Lay read sequences alongside the reference space, using their CIGARs
setops-methods

Set operations on GAlignments objects
stackStringsFromBam

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

Perform overlap queries between reads and genomic features
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
mapCoords-methods

Mapping ranges between sequences
cigar-utils

CIGAR utility functions
mapToAlignments

Map range coordinates between reads and genome space using CIGAR alignments
OverlapEncodings-class

OverlapEncodings objects
intra-range-methods

Intra range transformations of a GAlignments or GAlignmentsList object
junctions-methods

Extract junctions from genomic alignments