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Package: gmapR
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Maintainer: Michael Lawrence <lawrence.michael@gene.com>
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License: Artistic-2.0
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Title: An R interface to the GMAP/GSNAP/GSTRUCT suite
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Type: Package
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Author: Cory Barr, Thomas Wu, Michael Lawrence
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Description: GSNAP and GMAP are a pair of tools to align short-read
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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.
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Version: 1.13.5
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Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
GenomicRanges (>= 1.17.12)
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Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
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GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),
tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel
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Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
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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
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GmapParam-class.R GsnapParam-class.R
GsnapOutput-class.R GmapOutput-class.R
atoiindex-command.R
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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
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