Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.22.4
Author: M. Carlson, H. Pages, 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 (>= 0.7.17), IRanges (>=
        2.3.21), GenomeInfoDb (>= 1.5.16), GenomicRanges (>= 1.21.32),
        AnnotationDbi (>= 1.27.9)
Imports: methods, utils, tools, DBI (>= 0.2-5), RSQLite (>= 0.8-1),
        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, RUnit, BiocStyle, knitr
Collate: utils.R TxDb-SELECT-helpers.R Ensembl.utils.R
        findCompatibleMarts.R TxDb-class.R FeatureDb-class.R makeTxDb.R
        makeTxDbFromUCSC.R makeTxDbFromBiomart.R makeTxDbFromGRanges.R
        makeTxDbFromGFF.R makeFeatureDbFromUCSC.R id2name.R
        transcripts.R transcriptsBy.R transcriptsByOverlaps.R
        transcriptLengths.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
        test_GenomicFeatures_package.R
VignetteBuilder: knitr
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
        GenomeAnnotation
NeedsCompilation: no
Packaged: 2015-11-05 02:09:27 UTC; biocbuild
Built: R 3.2.2; ; 2016-03-19 11:20:30 UTC; unix
