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Bioconductor - gmapR (development version)

gmapR

This is the development version of gmapR; for the stable release version, see gmapR.

An R interface to the GMAP/GSNAP/GSTRUCT suite

Bioconductor version: Development (3.22)

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 gene.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("gmapR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gmapR")
Details biocViews Alignment, Software Version 1.51.0 In Bioconductor since BioC 2.11 (R-2.15) (13 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, BiocIO System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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