gmapR

This is the released version of gmapR; for the devel version, see gmapR.

An R interface to the GMAP/GSNAP/GSTRUCT suite

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DOI: 10.18129/B9.bioc.gmapR

Bioconductor version: Release (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 <lawremi at gmail.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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Software

Version 1.51.1

In Bioconductor since BioC 2.11 (R-2.15) (13 years)

License Artistic-2.0

Depends R (>= 2.15.0), methods, Seqinfo, GenomicRanges(>= 1.61.1), 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

Suggests GenomeInfoDb, 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

Imports Me

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_1.51.1.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) gmapR_1.51.1.tgz

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/

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