SeqArray

DOI: 10.18129/B9.bioc.SeqArray  

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

Bioconductor version: Release (3.16)

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 u.washington.edu>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DataRepresentation, Genetics, Infrastructure, Sequencing, Software
Version	1.38.0
In Bioconductor since	BioC 2.12 (R-3.0) (10 years)
License	GPL-3
Depends	R (>= 3.5.0), gdsfmt(>= 1.31.1)
Imports	methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
LinkingTo	gdsfmt
Suggests	Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation
SystemRequirements
Enhances
URL	https://github.com/zhengxwen/SeqArray
BugReports	https://github.com/zhengxwen/SeqArray/issues
Depends On Me	GBScleanR, SAIGEgds, SeqVarTools
Imports Me	GDSArray, GENESIS, ggmanh, VariantExperiment
Suggests Me	DelayedDataFrame, HIBAG, VCFArray
Links To Me
Build Report

Package Archives

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

Source Package	SeqArray_1.38.0.tar.gz
Windows Binary	SeqArray_1.38.0.zip
macOS Binary (x86_64)	SeqArray_1.38.0.tgz
macOS Binary (arm64)	SeqArray_1.38.0.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/
Package Downloads Report	Download Stats