Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.14.2
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 (>= 1.17.13), GenomicRanges
        (>= 1.13.16), AnnotationDbi (>= 1.23.14)
Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics,
        IRanges, GenomicRanges, Biostrings (>= 2.23.2), rtracklayer (>=
        1.15.1), biomaRt (>= 2.17.1), RCurl, utils, Biobase (>= 2.15.1)
Suggests: rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome,
        BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14),
        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.hg18.knownGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), Rsamtools,
        pasillaBamSubset (>= 0.0.5), seqnames.db, RUnit
Collate: utils.R Ensembl.utils.R TranscriptDb-class.R FeatureDb-class.R
        makeTranscriptDb.R makeTranscriptDbFromUCSC.R
        makeTranscriptDbFromBiomart.R makeTranscriptDbFromGFF.R
        makeFeatureDbFromUCSC.R saveFeatures.R id2name.R transcripts.R
        transcriptsByOverlaps.R transcriptsBy.R regions.R features.R
        extractTranscriptsFromGenome.R makeTxDbPackage.R
        seqnames-methods.R select-methods.R nearest-methods.R
        getPromoterSeq-methods.R test_GenomicFeatures_package.R
biocViews: Genetics, Infrastructure, Annotation,
        HighThroughputSequencing
Packaged: 2013-11-18 04:54:28 UTC; biocbuild
Built: R 3.0.2; ; 2013-12-29 11:11:38 UTC; unix
