Rsamtools
This is the released version of Rsamtools; for the devel version, see Rsamtools.
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | |
| - YouTube | Video |
Details
| biocViews | Alignment, Coverage, DataImport, QualityControl, Sequencing, Software |
| Version | 2.28.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (16.5 years) |
| License | Artistic-2.0 | file LICENSE |
| Depends | R (>= 3.5.0), methods, Seqinfo, GenomicRanges(>= 1.61.1), Biostrings(>= 2.77.2) |
| Imports | utils, BiocGenerics(>= 0.25.1), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), XVector(>= 0.19.7), 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_2.28.0.tar.gz |
| Windows Binary (x86_64) | Rsamtools_2.28.0.zip |
| macOS Binary (big-sur-x86_64) | Rsamtools_2.28.0.tgz |
| macOS Binary (sonoma-arm64) | Rsamtools_2.28.0.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 |