SeqArray

This is the released version of SeqArray; for the devel version, see SeqArray.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12

Data management of large-scale whole-genome sequence variant calls using GDS files

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-1390-0708 , Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb]

Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>

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

Xiuwen Zheng, Stephanie Gogarten. SeqArray: Data management of large-scale whole-genome sequence variant calls using GDS files. doi:10.18129/B9.bioc.SeqArray, R package version 1.52.1, https://bioconductor.org/packages/SeqArray.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("SeqArray")

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("SeqArray")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Genetics, Infrastructure, Sequencing, Software
Version	1.52.1
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 years)
License	GPL-3
Depends	R (>= 3.5.0), gdsfmt (>= 1.31.1)
Imports	methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, Seqinfo, Biostrings
System Requirements
URL	https://github.com/zhengxwen/SeqArray
Bug Reports	https://github.com/zhengxwen/SeqArray/issues

Suggests	Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation
Linking To	gdsfmt
Enhances
Depends On Me	GBScleanR, SAIGEgds, SeqVarTools
Imports Me	GDSArray, GENESIS, ggmanh, VariantExperiment
Suggests Me	DelayedDataFrame, GMMAT, HIBAG, MAGEE, VCFArray
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SeqArray_1.52.1.tar.gz
Windows Binary (x86_64)	SeqArray_1.52.1.zip
macOS Binary (big-sur-x86_64)	SeqArray_1.52.1.tgz
macOS Binary (sonoma-arm64)	SeqArray_1.52.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SeqArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SeqArray
Package Short Url	https://bioconductor.org/packages/SeqArray/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive