alabaster.vcf

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

Save and Load Variant Data to/from File

Bioconductor version: Development (3.23)

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>

Citation (from within R, enter citation("alabaster.vcf")):

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("alabaster.vcf")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, Software
Version	1.9.0
In Bioconductor since	BioC 3.17 (R-4.3) (2.5 years)
License	MIT + file LICENSE
Depends	alabaster.base, VariantAnnotation
Imports	methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools
System Requirements
URL

Suggests	knitr, rmarkdown, BiocStyle, testthat
Linking To
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
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/alabaster.vcf
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/alabaster.vcf
Package Short Url	https://bioconductor.org/packages/alabaster.vcf/
Package Downloads Report	Download Stats