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

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

Bioconductor version: Development (3.20)

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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

VariantExperiment-class HTML R Script
Reference Manual PDF


biocViews Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software
Version 1.19.2
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
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Source Package VariantExperiment_1.19.2.tar.gz
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