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 (3.21)
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("alabaster.vcf")):
Installation
To install this package, start R (version "4.5") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("alabaster.vcf")| Saving and loading VCFs | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | alabaster.base, VariantAnnotation |
| Imports | methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | alabaster |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | alabaster.vcf_1.7.0.tar.gz |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/alabaster.vcf/ |
| Package Short Url | https://bioconductor.org/packages/alabaster.vcf/ |
| Package Downloads Report | Download Stats |