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gmapR

An R interface to the GMAP/GSNAP/GSTRUCT suite


Bioconductor version: Release (3.18)

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 "4.3") and enter:


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

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")
gmapR PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Software
Version 1.44.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 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
System Requirements
URL
See More
Suggests RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
Linking To
Enhances
Depends On Me HTSeqGenie
Imports Me MMAPPR2
Suggests Me VariantTools, VariantToolsData
Links To Me
Build Report Build Report

Package Archives

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

Source Package gmapR_1.44.0.tar.gz
Windows Binary
macOS Binary (x86_64) gmapR_1.44.0.tgz
macOS Binary (arm64) gmapR_1.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gmapR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gmapR
Bioc Package Browser https://code.bioconductor.org/browse/gmapR/
Package Short Url https://bioconductor.org/packages/gmapR/
Package Downloads Report Download Stats