Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioconductor version: Release (3.20)
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Author: Martin Morgan [aut], Hervé Pagès [aut], Valerie Obenchain [aut], Nathaniel Hayden [aut], Busayo Samuel [ctb] (Converted Rsamtools vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("Rsamtools")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rsamtools")
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("Rsamtools")
An Introduction to Rsamtools | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text | |
Video |
Details
biocViews | Alignment, Coverage, DataImport, QualityControl, Sequencing, Software |
Version | 2.22.0 |
In Bioconductor since | BioC 2.6 (R-2.11) (14.5 years) |
License | Artistic-2.0 | file LICENSE |
Depends | methods, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.31.8), Biostrings(>= 2.47.6), R (>= 3.5.0) |
Imports | utils, BiocGenerics(>= 0.25.1), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), XVector(>= 0.19.7), zlibbioc, bitops, BiocParallel, stats |
System Requirements | GNU make |
URL | https://bioconductor.org/packages/Rsamtools |
Bug Reports | https://github.com/Bioconductor/Rsamtools/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | Rsamtools_2.22.0.tar.gz |
Windows Binary (x86_64) | Rsamtools_2.22.0.zip (64-bit only) |
macOS Binary (x86_64) | Rsamtools_2.22.0.tgz |
macOS Binary (arm64) | Rsamtools_2.21.2.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/Rsamtools |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rsamtools |
Bioc Package Browser | https://code.bioconductor.org/browse/Rsamtools/ |
Package Short Url | https://bioconductor.org/packages/Rsamtools/ |
Package Downloads Report | Download Stats |