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>

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

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

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