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 (3.24)
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 <alexchwong.github at gmail.com>
citation("ompBAM")):Alex Chit Hei Wong. ompBAM: C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files. doi:10.18129/B9.bioc.ompBAM, R package version 1.17.0, https://bioconductor.org/packages/ompBAM.
Generated from the package metadata; it may differ from the package's own citation.
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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, DataImport, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | utils, Rcpp |
| 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 | BamScale, SpliceWiz |
| Suggests Me | |
| Links To Me | BamScale, SpliceWiz |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ompBAM_1.17.0.tar.gz |
| Windows Binary (x86_64) | ompBAM_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | ompBAM_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | ompBAM_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ompBAM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ompBAM |
| Package Short Url | https://bioconductor.org/packages/ompBAM/ |
| Package Downloads Report | Download Stats |