ompBAM

DOI: 10.18129/B9.bioc.ompBAM  

C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files

Bioconductor version: Release (3.16)

This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.

Author: Alex Chit Hei Wong [aut, cre, cph]

Maintainer: Alex Chit Hei Wong <a.wong at centenary.org.au>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("ompBAM")

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("ompBAM")

 

HTML	R Script	ompBAM API Documentation
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, DataImport, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends
Imports	utils, Rcpp, zlibbioc
LinkingTo
Suggests	RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/alexchwong/ompBAM
BugReports	https://support.bioconductor.org/
Depends On Me
Imports Me	SpliceWiz
Suggests Me
Links To Me	SpliceWiz
Build Report

Package Archives

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

Source Package	ompBAM_1.2.0.tar.gz
Windows Binary	ompBAM_1.2.0.zip
macOS Binary (x86_64)	ompBAM_1.2.0.tgz
macOS Binary (arm64)	ompBAM_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ompBAM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ompBAM
Bioc Package Browser	https://code.bioconductor.org/browse/ompBAM/
Package Short Url	https://bioconductor.org/packages/ompBAM/
Package Downloads Report	Download Stats