Rhtslib
This is the development version of Rhtslib; for the stable release version, see Rhtslib.
HTSlib high-throughput sequencing library as an R package
Bioconductor version: Development (3.24)
This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").
Author: Nathaniel Hayden [led, aut], Martin Morgan [aut], Hervé Pagès [aut, cre], Tomas Kalibera [ctb], Jeroen Ooms [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("Rhtslib")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Rhtslib")
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("Rhtslib")| Motivation and use of Rhtslib | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Sequencing, Software |
| Version | 3.9.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | LGPL (>= 2) |
| Depends | |
| Imports | tools |
| System Requirements | libbz2 & liblzma & libcurl (with header files), GNU make |
| URL | https://bioconductor.org/packages/Rhtslib http://www.htslib.org/ |
| Bug Reports | https://github.com/Bioconductor/Rhtslib/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | deepSNV, diffHic, maftools, mitoClone2, scPipe, stPipe |
| Suggests Me | |
| Links To Me | bamsignals, csaw, deepSNV, DiffBind, diffHic, epialleleR, FLAMES, h5vc, iscream, maftools, methylKit, mitoClone2, podkat, QuasR, raer, Rfastp, Rsamtools, scPipe, ShortRead, stPipe, VariantAnnotation, jackalope |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Rhtslib_3.9.0.tar.gz |
| Windows Binary (x86_64) | Rhtslib_3.9.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Rhtslib_3.9.0.tgz |
| macOS Binary (sonoma-arm64) | Rhtslib_3.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rhtslib |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rhtslib |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rhtslib/ |
| Package Short Url | https://bioconductor.org/packages/Rhtslib/ |
| Package Downloads Report | Download Stats |