GenomicAlignments v1.8.4

Representation and manipulation of short genomic alignments

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.

Functions in GenomicAlignments

Name Description
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
pileLettersAt 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-utils CIGAR utility functions
mapToAlignments Map range coordinates between reads and genome space using CIGAR alignments
readGAlignments Reading genomic alignments from a file
sequenceLayer Lay read sequences alongside the reference space, using their CIGARs
findMateAlignment Pairing the elements of a GAlignments object
setops-methods Set operations on GAlignments objects
stackStringsFromBam Stack the read sequences stored in a BAM file on a region of interest
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Encoding UTF-8
biocViews Genetics, Infrastructure, DataImport, Sequencing, RNASeq, SNP, Coverage, Alignment
LinkingTo S4Vectors, IRanges
License Artistic-2.0
Collate cigar-utils.R GAlignments-class.R GAlignmentPairs-class.R GAlignmentsList-class.R GappedReads-class.R OverlapEncodings-class.R findMateAlignment.R readGAlignments.R junctions-methods.R sequenceLayer.R pileLettersAt.R stackStringsFromBam.R intra-range-methods.R coverage-methods.R setops-methods.R findOverlaps-methods.R coordinate-mapping-methods.R encodeOverlaps-methods.R findCompatibleOverlaps-methods.R summarizeOverlaps-methods.R findSpliceOverlaps-methods.R zzz.R
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