SeqArray

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

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

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DOI: 10.18129/B9.bioc.SeqArray

Bioconductor version: Release (3.22)

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 iD 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")):

Installation

To install this package, start R (version "4.5") 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")

R Integration HTML R Script

SeqArray Data Format and Access HTML R Script

SeqArray Overview HTML

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Genetics, Infrastructure, Sequencing, Software

Version 1.50.0

In Bioconductor since BioC 2.12 (R-3.0) (12.5 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, HIBAG, VCFArray, GMMAT, MAGEE

Links To Me

Build Report Build Report

Package Archives

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

Source Package SeqArray_1.50.0.tar.gz

Windows Binary (x86_64) SeqArray_1.49.4.zip

macOS Binary (x86_64) SeqArray_1.50.0.tgz

macOS Binary (arm64) SeqArray_1.50.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SeqArray

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SeqArray

Bioc Package Browser https://code.bioconductor.org/browse/SeqArray/

Package Short Url https://bioconductor.org/packages/SeqArray/

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