gmapR

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see gmapR.

An R interface to the GMAP/GSNAP/GSTRUCT suite

Bioconductor version: 3.14

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 "4.1") 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 1.36.0

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

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_1.36.0.tar.gz

Windows Binary

macOS 10.13 (High Sierra) gmapR_1.36.0.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

Old Source Packages for BioC 3.14 Source Archive