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VariantExperiment

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend


Bioconductor version: Release (3.19)

VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.

Author: Qian Liu [aut, cre], Hervé Pagès [aut], Martin Morgan [aut]

Maintainer: Qian Liu <Qian.Liu at roswellpark.org>

Citation (from within R, enter citation("VariantExperiment")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("VariantExperiment")

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("VariantExperiment")
VariantExperiment-class HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software
Version 1.18.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.6.0), S4Vectors(>= 0.21.24), SummarizedExperiment(>= 1.13.0), GenomicRanges
Imports GDSArray(>= 1.11.1), DelayedDataFrame(>= 1.6.0), tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, DelayedArray, Biostrings, IRanges
System Requirements
URL https://github.com/Bioconductor/VariantExperiment
Bug Reports https://github.com/Bioconductor/VariantExperiment/issues
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Suggests testthat, knitr, rmarkdown, markdown, BiocStyle
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Package Archives

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

Source Package VariantExperiment_1.18.1.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/VariantExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantExperiment
Bioc Package Browser https://code.bioconductor.org/browse/VariantExperiment/
Package Short Url https://bioconductor.org/packages/VariantExperiment/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive