DESCRIPTION

Package: GenomicAlignments
Title: 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.
biocViews: Infrastructure, DataImport, Genetics, Sequencing, RNASeq, SNP,
	Coverage, Alignment, ImmunoOncology
URL: https://bioconductor.org/packages/GenomicAlignments
Video: https://www.youtube.com/watch?v=2KqBSbkfhRo , https://www.youtube.com/watch?v=3PK_jx44QTs
BugReports: https://github.com/Bioconductor/GenomicAlignments/issues
Version: 1.45.0
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
	person("Hervé", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("Valerie", "Obenchain", role="aut"),
	person("Martin", "Morgan", role="aut"),
	person("Fedor", "Bezrukov", role="ctb"),
	person("Robert", "Castelo", role="ctb"),
	person("Halimat C.", "Atanda", role="ctb",
		comment="Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML."
	))
Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0),
	S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1),
	GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13),
	Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2)
Imports: methods, utils, stats, BiocGenerics, S4Vectors,
	IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel
LinkingTo: S4Vectors, IRanges
Suggests: 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, knitr, BiocStyle
Collate: 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
VignetteBuilder: knitr