DOI: 10.18129/B9.bioc.SeqArray    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see SeqArray.

Data Management of Large-scale Whole-genome Sequence Variant Calls

Bioconductor version: 3.10

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 "3.6") and enter:

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


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:



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


biocViews DataRepresentation, Genetics, Infrastructure, Sequencing, Software
Version 1.26.2
In Bioconductor since BioC 2.12 (R-3.0) (7 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.18.0)
Imports methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
LinkingTo gdsfmt
Suggests Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation
Depends On Me SAIGEgds, SeqVarTools
Imports Me GDSArray, GENESIS, VariantExperiment
Suggests Me DelayedDataFrame, VCFArray
Links To Me
Build Report  

Package Archives

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

Source Package SeqArray_1.26.2.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) SeqArray_1.26.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: