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

Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Bioconductor version: Development (3.20)

Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

Author: Xiuwen Zheng [aut, cre] , Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb]

Maintainer: Xiuwen Zheng <zhengx at>

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


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:

R Integration HTML R Script
SeqArray Data Format and Access HTML R Script
SeqArray Overview HTML
Reference Manual PDF


biocViews DataRepresentation, Genetics, Infrastructure, Sequencing, Software
Version 1.45.0
In Bioconductor since BioC 2.12 (R-3.0) (11.5 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.31.1)
Imports methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
System Requirements
Bug Reports
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Suggests Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation
Linking To gdsfmt
Depends On Me GBScleanR, SAIGEgds, SeqVarTools
Imports Me GDSArray, GENESIS, ggmanh, VariantExperiment
Suggests Me DelayedDataFrame, HIBAG, VCFArray, GMMAT, MAGEE
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package SeqArray_1.45.0.tar.gz
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macOS Binary (x86_64) SeqArray_1.45.0.tgz
macOS Binary (arm64) SeqArray_1.45.0.tgz
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