alabaster.vcf

DOI: 10.18129/B9.bioc.alabaster.vcf  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see alabaster.vcf.

Save and Load Variant Data to/from File

Bioconductor version: 3.17

Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

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

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

BiocManager::install("alabaster.vcf")

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("alabaster.vcf")

 

HTML	R Script	Saving and loading VCFs
PDF		Reference Manual
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, Software
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	alabaster.base, VariantAnnotation
Imports	methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	alabaster
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	alabaster.vcf_1.0.0.tar.gz
Windows Binary	alabaster.vcf_1.0.0.zip
macOS Binary (x86_64)	alabaster.vcf_1.0.0.tgz
macOS Binary (arm64)	alabaster.vcf_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/alabaster.vcf
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/alabaster.vcf
Bioc Package Browser	https://code.bioconductor.org/browse/alabaster.vcf/
Package Short Url	https://bioconductor.org/packages/alabaster.vcf/
Package Downloads Report	Download Stats