Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.18.7
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 (>= 0.1.5), IRanges (>=
        1.99.1), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.12),
        AnnotationDbi (>= 1.27.9)
Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), Biostrings (>=
        2.23.3), rtracklayer (>= 1.26.3), biomaRt (>= 2.17.1), RCurl,
        utils, Biobase (>= 2.15.1)
Suggests: org.Mm.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), Rsamtools,
        pasillaBamSubset (>= 0.0.5), RUnit, BiocStyle, knitr
Collate: utils.R Ensembl.utils.R findCompatibleMarts.R TxDb-class.R
        FeatureDb-class.R makeTranscriptDb.R makeTranscriptDbFromUCSC.R
        makeTranscriptDbFromBiomart.R makeTranscriptDbFromGFF.R
        makeFeatureDbFromUCSC.R id2name.R transcripts.R
        transcriptsByOverlaps.R transcriptsBy.R features.R
        extractUpstreamSeqs.R extractTranscriptSeqs.R
        transcriptLocs2refLocs.R makeTxDbPackage.R seqnames-methods.R
        select-methods.R nearest-methods.R getPromoterSeq-methods.R
        extractTranscriptsFromGenome.R test_GenomicFeatures_package.R
VignetteBuilder: knitr
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
        GenomeAnnotation
Packaged: 2015-04-08 02:27:01 UTC; biocbuild
Built: R 3.1.3; ; 2015-04-08 08:29:56 UTC; windows
