Package: GenomicFeatures
Title: Query the gene models of a given organism/assembly
Description: Extract the genomic locations of genes, transcripts, exons,
	introns, and CDS, for the gene models stored in a TxDb object.
	A TxDb object is a small database that contains the gene models of
	a given organism/assembly. Bioconductor provides a small collection
	of TxDb objects in the form of ready-to-install TxDb packages for
	the most commonly studied organisms. Additionally, the user can
	easily make a TxDb object (or package) for the organism/assembly
	of their choice by using the tools from the txdbmaker package.
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
	GenomeAnnotation
URL: https://bioconductor.org/packages/GenomicFeatures
BugReports: https://github.com/Bioconductor/GenomicFeatures/issues
Version: 1.63.1
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
	person("H.", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("M.", "Carlson", role="aut"),
	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 (>= 0.51.2), S4Vectors (>= 0.47.6),
	IRanges (>= 2.37.1), Seqinfo (>= 0.99.2),
	GenomicRanges (>= 1.61.1), AnnotationDbi (>= 1.41.4)
Imports: methods, utils, stats, DBI, XVector, Biostrings (>= 2.77.2),
	rtracklayer (>= 1.69.1)
Suggests: GenomeInfoDb, txdbmaker, 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),
	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
	TxDb-class.R FeatureDb-class.R
	mapIdsToRanges.R
	id2name.R
	transcripts.R
	transcriptsBy.R
	transcriptsByOverlaps.R
	transcriptLengths.R
	exonicParts.R
	extendExonsIntoIntrons.R
	features.R
	tRNAs.R
	extractTranscriptSeqs.R
	extractUpstreamSeqs.R
	getPromoterSeq-methods.R
	select-methods.R
	nearest-methods.R
	transcriptLocs2refLocs.R
	coordinate-mapping-methods.R
	proteinToGenome.R
	coverageByTranscript.R
	zzz.R
git_url: https://git.bioconductor.org/packages/GenomicFeatures
git_branch: devel
git_last_commit: d92f2d0
git_last_commit_date: 2025-10-30
Repository: Bioconductor 3.23
