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.
Herv\'e Pag\`es, Valerie Obenchain, Martin Morgan
Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
SNP, Coverage, Alignment
R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>=
0.8.6), IRanges (>= 2.3.21), GenomeInfoDb (>= 1.1.20),
GenomicRanges (>= 1.21.6), SummarizedExperiment (>= 0.3.1),
Biostrings (>= 2.37.1), Rsamtools (>= 1.21.4)
methods, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
ShortRead, rtracklayer, BSgenome, GenomicFeatures,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19,
DESeq, edgeR, RUnit, BiocStyle
utils.R 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 mapCoords-methods.R
coordinate-mapping-methods.R encodeOverlaps-methods.R
findCompatibleOverlaps-methods.R summarizeOverlaps-methods.R
findSpliceOverlaps-methods.R zzz.R