Package: gmapR
Maintainer: Michael Lawrence <lawrence.michael@gene.com>
License: Artistic-2.0
Title: An R interface to the GMAP/GSNAP/GSTRUCT suite
Type: Package
Author: Cory Barr, Thomas Wu, Michael Lawrence
Description: GSNAP and GMAP are a pair of tools to align short-read
        data written by Tom Wu.  This package provides convenience
        methods to work with GMAP and GSNAP from within R. In addition,
        it provides methods to tally alignment results on a
        per-nucleotide basis using the bam_tally tool.
Version: 1.10.0
Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
        GenomicRanges (>= 1.17.12)
Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),
        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
        BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
        TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
        LungCancerLines
Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
        GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
        GsnapParam-class.R GsnapOutput-class.R atoiindex-command.R
        BamTallyParam-class.R bam_tally-command.R cmetindex-command.R
        get-genome-command.R gmap-command.R gmap_build-command.R
        gsnap-command.R iit-format.R iit_store-command.R info.R
        snpindex-command.R system.R test_gmapR_package.R
        makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R
biocViews: Alignment