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Rhtslib

HTSlib high-throughput sequencing library as an R package


Bioconductor version: Release (3.18)

This package provides version 1.15.1 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], Jeroen Ooms [ctb]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("Rhtslib")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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 PDF
NEWS Text

Details

biocViews DataImport, Sequencing, Software
Version 2.4.1
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License LGPL (>= 2)
Depends
Imports zlibbioc
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 zlibbioc
Enhances
Depends On Me
Imports Me deepSNV, diffHic, maftools, mitoClone2, scPipe
Suggests Me
Links To Me bamsignals, csaw, deepSNV, DiffBind, diffHic, epialleleR, FLAMES, h5vc, maftools, methylKit, mitoClone2, podkat, qrqc, QuasR, raer, Rfastp, Rsamtools, scPipe, seqbias, ShortRead, TransView, VariantAnnotation
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Rhtslib_2.4.1.tar.gz
Windows Binary Rhtslib_2.4.1.zip
macOS Binary (x86_64) Rhtslib_2.4.1.tgz
macOS Binary (arm64) Rhtslib_2.4.1.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
Old Source Packages for BioC 3.18 Source Archive