Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.30.0
Encoding: UTF-8
Author: M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan,
	D. Sarkar, M. Lawrence
License: Artistic-2.0
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.
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.47), IRanges (>=
        2.11.16), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.29.14),
        AnnotationDbi (>= 1.33.15)
Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RMySQL,
        RCurl, XVector, Biostrings (>= 2.23.3), rtracklayer (>=
        1.29.24), biomaRt (>= 2.17.1), Biobase (>= 2.15.1)
Suggests: org.Mm.eg.db, org.Hs.eg.db, BSgenome,
        BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
        BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>=
        1.3.17), mirbase.db, FDb.UCSC.tRNAs,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1),
        TxDb.Mmusculus.UCSC.mm10.knownGene,
        TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        SNPlocs.Hsapiens.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset
        (>= 0.0.5), GenomicAlignments, ensembldb, RUnit, BiocStyle,
        knitr
Collate: utils.R TxDb-schema.R TxDb-SELECT-helpers.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
        disjointExons.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
        coverageByTranscript.R zzz.R
VignetteBuilder: knitr
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
        GenomeAnnotation
NeedsCompilation: no
Packaged: 2017-10-30 22:56:58 UTC; biocbuild
