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SeqArray

This is the development version of SeqArray; for the stable release version, see SeqArray.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataRepresentation, Genetics, Infrastructure, Sequencing, Software
Version 1.43.3
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.31.1)
Imports methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
System Requirements
URL https://github.com/zhengxwen/SeqArray
Bug Reports https://github.com/zhengxwen/SeqArray/issues
See More
Suggests Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, 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
Links To Me
Build Report Build Report

Package Archives

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

Source Package SeqArray_1.43.3.tar.gz
Windows Binary SeqArray_1.43.3.zip (64-bit only)
macOS Binary (x86_64) SeqArray_1.43.3.tgz
macOS Binary (arm64) SeqArray_1.43.2.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