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ompBAM

This is the development version of ompBAM; for the stable release version, see ompBAM.

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


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, DataImport, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends
Imports utils, Rcpp, zlibbioc
System Requirements
URL https://github.com/alexchwong/ompBAM
Bug Reports https://support.bioconductor.org/
See More
Suggests RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me SpliceWiz
Suggests Me
Links To Me SpliceWiz
Build Report Build Report

Package Archives

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

Source Package ompBAM_1.7.0.tar.gz
Windows Binary ompBAM_1.7.0.zip
macOS Binary (x86_64) ompBAM_1.7.0.tgz
macOS Binary (arm64) ompBAM_1.7.0.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