BamScale
This is the development version of BamScale; to use it, please install the devel version of Bioconductor.
Bioconductor-Friendly Multithreaded BAM Processing
Bioconductor version: Development (3.24)
Multithreaded sequential BAM processing built on top of the ompBAM C++ engine. BamScale provides user-friendly BAM read and scan interfaces designed for compatibility with existing Bioconductor workflows.
Author: Chirag Parsania [aut, cre]
Maintainer: Chirag Parsania <chirag.parsania at gmail.com>
citation("BamScale")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("BamScale")
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("BamScale")| Benchmarking BamScale Across Step1, GAlignments, and SeqQual Workloads | HTML | R Script |
| Getting started with BamScale | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Alignment, Coverage, DataImport, QualityControl, Sequencing, Software |
| Version | 0.99.10 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | BiocGenerics, BiocParallel, Biostrings, GenomicAlignments, GenomicRanges, IRanges, methods, ompBAM, Rcpp, Rsamtools, S4Vectors |
| System Requirements | C++17, OpenMP |
| URL | https://cparsania.github.io/BamScale/ |
| Bug Reports | https://github.com/cparsania/BamScale/issues |
See More
| Suggests | BiocStyle, chipseqDBData, dplyr, ExperimentHub, GenomeInfoDb, ggplot2, knitr, readr, rmarkdown, scales, tibble, testthat (>= 3.0.0), tidyr |
| Linking To | Rcpp, ompBAM |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BamScale_0.99.10.tar.gz |
| Windows Binary (x86_64) | BamScale_0.99.10.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BamScale_0.99.10.tgz |
| macOS Binary (sonoma-arm64) | BamScale_0.99.10.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BamScale |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BamScale |
| Bioc Package Browser | https://code.bioconductor.org/browse/BamScale/ |
| Package Short Url | https://bioconductor.org/packages/BamScale/ |
| Package Downloads Report | Download Stats |