gmapR : An R interface to the GMAP/GSNAP/GSTRUCT suite

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: 1.14.0
Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges
(>= 1.17.12), Rsamtools (>= 1.17.8)
Imports: S4Vectors (>= 0.9.25), IRanges, rtracklayer (>= 1.31.2),
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
GmapParam-class.R GsnapParam-class.R GsnapOutput-class.R
GmapOutput-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
NeedsCompilation: yes
Packaged: 2016-05-04 04:43:44 UTC; biocbuild