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An R interface to the GMAP/GSNAP/GSTRUCT suite

Bioconductor version: Release (3.1)

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.

Author: Cory Barr, Thomas Wu, Michael Lawrence

Maintainer: Michael Lawrence <lawrence.michael at>

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PDF R Script gmapR
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Software
Version 1.10.0
In Bioconductor since BioC 2.11 (R-2.15) (3 years)
License Artistic-2.0
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,, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
Depends On Me HTSeqGenie
Imports Me VariantTools
Suggests Me
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