DOI: 10.18129/B9.bioc.gmapR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see gmapR.

An R interface to the GMAP/GSNAP/GSTRUCT suite

Bioconductor version: 3.16

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 <michafla at>

Citation (from within R, enter citation("gmapR")):


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PDF R Script gmapR
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biocViews Alignment, Software
Version 1.40.0
In Bioconductor since BioC 2.11 (R-2.15) (10.5 years)
License Artistic-2.0
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,, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
Depends On Me HTSeqGenie
Imports Me MMAPPR2
Suggests Me VariantTools, VariantToolsData
Links To Me
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