Package: GenomicFeatures
Title: Conveniently import and query gene models
Description: A set of tools and methods for making and manipulating
	transcript centric annotations. With these tools the user can
	easily download the genomic locations of the transcripts, exons
	and cds of a given organism, from either the UCSC Genome
	Browser or a BioMart database (more sources will be supported
	in the future). This information is then stored in a local
	database that keeps track of the relationship between
	transcripts, exons, cds and genes. Flexible methods are
	provided for extracting the desired features in a convenient
	format.
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
	GenomeAnnotation
URL: https://bioconductor.org/packages/GenomicFeatures
BugReports: https://github.com/Bioconductor/GenomicFeatures/issues
Version: 1.55.1
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
	person("M.", "Carlson", role="aut"),
	person("H.", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("P.", "Aboyoun", role="aut"),
	person("S.", "Falcon", role="aut"),
	person("M.", "Morgan", role="aut"),
	person("D.", "Sarkar", role="aut"),
	person("M.", "Lawrence", role="aut"),
	person("V.", "Obenchain", role="aut"),
	person("S.", "Arora", role="ctb"),
	person("J.", "MacDonald", role="ctb"),
	person("M.", "Ramos", role="ctb"),
	person("S.", "Saini", role="ctb"),
	person("P.", "Shannon", role="ctb"),
	person("L.", "Shepherd", role="ctb"),
	person("D.", "Tenenbaum", role="ctb"),
	person("D.", "Van Twisk", role="ctb"))
Depends: R (>= 3.5.0), BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29),
	IRanges (>= 2.13.23), GenomeInfoDb (>= 1.35.8),
	GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4)
Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
	XVector (>= 0.19.7), Biostrings (>= 2.47.6), BiocIO,
	rtracklayer (>= 1.51.5), biomaRt (>= 2.17.1), Biobase (>= 2.15.1)
Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db,
	BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
	BSgenome.Celegans.UCSC.ce11,
	BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17),
	mirbase.db, FDb.UCSC.tRNAs,
	TxDb.Hsapiens.UCSC.hg19.knownGene,
	TxDb.Celegans.UCSC.ce11.ensGene,
	TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1),
	TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7),
	TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
	TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6),
	SNPlocs.Hsapiens.dbSNP144.GRCh38,
	Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7),
	ensembldb, AnnotationFilter,
	RUnit, BiocStyle, knitr, markdown
VignetteBuilder: knitr
Collate: utils.R
	TxDb-schema.R
	TxDb-SELECT-helpers.R
	UCSC-utils.R
	Ensembl-utils.R findCompatibleMarts.R
	TxDb-class.R FeatureDb-class.R
	makeTxDb.R
	makeTxDbFromUCSC.R
	makeTxDbFromBiomart.R
	makeTxDbFromEnsembl.R
	makeTxDbFromGRanges.R
	makeTxDbFromGFF.R
	makeFeatureDbFromUCSC.R
	mapIdsToRanges.R
	id2name.R
	transcripts.R
	transcriptsBy.R
	transcriptsByOverlaps.R
	transcriptLengths.R
	exonicParts.R
	extendExonsIntoIntrons.R
	features.R
	microRNAs.R
	extractTranscriptSeqs.R
	extractUpstreamSeqs.R
	getPromoterSeq-methods.R
	makeTxDbPackage.R
	select-methods.R
	nearest-methods.R
	transcriptLocs2refLocs.R
	coordinate-mapping-methods.R
	proteinToGenome.R
	coverageByTranscript.R
	zzz.R
