gmapR

DOI: 10.18129/B9.bioc.gmapR  

An R interface to the GMAP/GSNAP/GSTRUCT suite

Bioconductor version: Release (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 gene.com>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	gmapR
PDF		Reference Manual
Text		NEWS

Details

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
LinkingTo
Suggests	RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
SystemRequirements
Enhances
URL
Depends On Me	HTSeqGenie
Imports Me	MMAPPR2
Suggests Me	VariantTools, VariantToolsData
Links To Me
Build Report

Package Archives

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

Source Package	gmapR_1.40.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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