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.
Infrastructure, DataImport, Genetics, Sequencing, RNASeq,
SNP, Coverage, Alignment, ImmunoOncology
c(
	person("Hervé", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("Valerie", "Obenchain", role="aut"),
	person("Martin", "Morgan", role="aut"))
methods, utils, 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,
DESeq2, 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 stackStringsFromGAlignments.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
Hervé Pagès [aut, cre],
  Valerie Obenchain [aut],
  Martin Morgan [aut]