DESCRIPTION

Package: GenomicRanges
Title: Representation and manipulation of genomic intervals
Description: The ability to efficiently represent and manipulate genomic
	annotations and alignments is playing a central role when it comes
	to analyzing high-throughput sequencing data (a.k.a. NGS data).
	The GenomicRanges package defines general purpose containers for
	storing and manipulating genomic intervals and variables defined along
	a genome. More specialized containers for representing and manipulating
	short alignments against a reference genome, or a matrix-like
	summarization of an experiment, are defined in the GenomicAlignments
	and SummarizedExperiment packages, respectively. Both packages build
	on top of the GenomicRanges infrastructure.
biocViews: Genetics, Infrastructure, DataRepresentation, Sequencing,
	Annotation, GenomeAnnotation, Coverage
URL: https://bioconductor.org/packages/GenomicRanges
BugReports: https://github.com/Bioconductor/GenomicRanges/issues
Version: 1.59.1
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
	person("Patrick", "Aboyoun", role="aut"),
	person("Hervé", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("Michael", "Lawrence", role="aut"),
	person("Sonali", "Arora", role="ctb"),
	person("Martin", "Morgan", role="ctb"),
	person("Kayla", "Morrell", role="ctb"),
	person("Valerie", "Obenchain", role="ctb"),
	person("Marcel", "Ramos", role="ctb"),
	person("Lori", "Shepherd", role="ctb"),
	person("Dan", "Tenenbaum", role="ctb"),
	person("Daniel", "van Twisk", role="ctb"))
Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2),
	S4Vectors (>= 0.45.2), IRanges (>= 2.41.1), GenomeInfoDb (>= 1.43.1)
Imports: utils, stats, XVector (>= 0.29.2)
LinkingTo: S4Vectors, IRanges
Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3),
	SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53),
	GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker,
	Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR,
	KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset,
	KEGGREST, hgu95av2.db, hgu95av2probe,
	BSgenome.Scerevisiae.UCSC.sacCer2,
	BSgenome.Hsapiens.UCSC.hg38,
	BSgenome.Mmusculus.UCSC.mm10,
	TxDb.Athaliana.BioMart.plantsmart22,
	TxDb.Dmelanogaster.UCSC.dm3.ensGene,
	TxDb.Hsapiens.UCSC.hg38.knownGene,
	TxDb.Mmusculus.UCSC.mm10.knownGene,
	RUnit, digest, knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
Collate: normarg-utils.R
	utils.R
	phicoef.R
	transcript-utils.R
	constraint.R
	strand-utils.R
	genomic-range-squeezers.R
	GenomicRanges-class.R
	GenomicRanges-comparison.R
	GRanges-class.R
	GPos-class.R
	GRangesFactor-class.R
	DelegatingGenomicRanges-class.R
	GNCList-class.R
	GenomicRangesList-class.R
	GRangesList-class.R
	makeGRangesFromDataFrame.R
	makeGRangesListFromDataFrame.R
	RangedData-methods.R
	findOverlaps-methods.R
	intra-range-methods.R
	inter-range-methods.R
	coverage-methods.R
	setops-methods.R
	subtract-methods.R
	nearest-methods.R
	absoluteRanges.R
	tileGenome.R
	tile-methods.R
	genomicvars.R
	zzz.R