gmapR
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see gmapR.
An R interface to the GMAP/GSNAP/GSTRUCT suite
Bioconductor version: 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>
citation("gmapR")):
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")| gmapR | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Software |
| Version | 1.40.0 |
| 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_1.40.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |