gmapR
An R interface to the GMAP/GSNAP/GSTRUCT suite
Bioconductor version: Release (3.19)
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("gmapR")
):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Alignment, Software |
Version | 1.46.0 |
In Bioconductor since | BioC 2.11 (R-2.15) (12 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 | |
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_1.46.0.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | gmapR_1.46.0.tgz |
macOS Binary (arm64) | gmapR_1.46.0.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 |