Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.8.3
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), IRanges (>= 1.13.10), GenomicRanges
        (>= 1.7.17), AnnotationDbi (>= 1.15.39)
Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics,
        IRanges, GenomicRanges, Biostrings (>= 2.23.2), rtracklayer (>=
        1.15.1), biomaRt, RCurl, utils, Biobase (>= 2.15.1)
Suggests: rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome,
        BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14),
        BSgenome.Celegans.UCSC.ce2, mirbase.db, FDb.UCSC.tRNAs, RUnit,
        TxDb.Hsapiens.UCSC.hg18.knownGene
Collate: AllClasses.R AllGenerics.R utils.R Ensembl.utils.R
        TranscriptDb-class.R FeatureDb-class.R makeTranscriptDb.R
        makeTranscriptDbFromUCSC.R makeTranscriptDbFromBiomart.R
        makeFeatureDbFromUCSC.R transcripts.R transcriptsByOverlaps.R
        transcriptsBy.R regions.R features.R
        extractTranscriptsFromGenome.R makeTxDbPackage.R
        methods-select.R test_GenomicFeatures_package.R
        spliceGraph_utils.R spliceGraph.R
biocViews: Genetics, Infrastructure, Annotation,
        HighThroughputSequencing
Packaged: 2012-08-24 06:08:13 UTC; biocbuild
Built: R 2.15.1; ; 2012-08-24 10:48:00 UTC; windows
