Package: gmapR
Maintainer: Michael Lawrence <michafla@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: 1.42.0
Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges
        (>= 1.31.8), Rsamtools (>= 1.31.2)
Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>=
        0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3),
        Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase,
        BSgenome, GenomicAlignments (>= 1.15.6), 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
        GmapParam-class.R GsnapParam-class.R GsnapOutput-class.R
        GmapOutput-class.R atoiindex-command.R iit-format.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_store-command.R info.R snpindex-command.R
        system.R test_gmapR_package.R makeGmapGenomePackage.R
        TP53Genome.R utils.R asSystemCall.R
biocViews: Alignment
git_url: https://git.bioconductor.org/packages/gmapR
git_branch: RELEASE_3_17
git_last_commit: 506bc70
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: yes
Packaged: 2023-04-25 21:21:16 UTC; biocbuild
Built: R 4.3.1; x86_64-conda-linux-gnu; 2023-07-14 21:47:26 UTC; unix
