Rsamtools
This is the development version of Rsamtools; for the stable release version, see Rsamtools.
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("Rsamtools")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| Video |
Details
| biocViews | Alignment, Coverage, DataImport, QualityControl, Sequencing, Software |
| Version | 2.25.3 |
| In Bioconductor since | BioC 2.6 (R-2.11) (15.5 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
| Suggests | GenomicAlignments, ShortRead(>= 1.19.10), GenomicFeatures, VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr |
| Linking To | Rhtslib(>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/Rsamtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rsamtools |
| Package Short Url | https://bioconductor.org/packages/Rsamtools/ |
| Package Downloads Report | Download Stats |