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gmapR (version 1.14.0)

An R interface to the GMAP/GSNAP/GSTRUCT suite

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.

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Version

Version

1.14.0

License

Artistic-2.0

Maintainer

Michael Lawrence

Last Published

February 15th, 2017

Functions in gmapR (1.14.0)

GmapSnpDirectory-class

Class "GmapSnpDirectory"
GmapGenome-class

Class "GmapGenome"
GmapSnps-class

Class "GmapSnps"
TP53Genome

Demo genome around TP53
internals

gmapR2 internals
GsnapOutput-class

Class "GsnapOutput"
directory

Get the Path to the Location on Disk from a gmapR Class
gsnap-methods

Align a Set of Reads Using the GSNAP Aligner
makeGmapGenomePackage

Function to create a GmapGenome package from a GmapGenome object
GsnapParam-class

Class "GsnapParam"
bam_tally-methods

Per-position Alignment Summaries
GmapGenomeDirectory-class

Class "GmapGenomeDirectory"
gmap_build-methods

Build Gmap/Gsnap Genome
BamTallyParam-class

Class "BamTallyParam"