SeqArray

DOI: 10.18129/B9.bioc.SeqArray    

This is the development version of SeqArray; to use it, please install the devel version of Bioconductor.

Data Management of Large-scale Whole-genome Sequence Variant Calls

Bioconductor version: Development (3.10)

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 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 <zhengxwen at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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 1.25.3
In Bioconductor since BioC 2.12 (R-3.0) (6.5 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.18.0)
Imports methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
LinkingTo gdsfmt
Suggests Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation
SystemRequirements
Enhances
URL http://github.com/zhengxwen/SeqArray
BugReports http://github.com/zhengxwen/SeqArray/issues
Depends On Me SAIGEgds, SeqVarTools
Imports Me GDSArray, GENESIS, VariantExperiment
Suggests Me DelayedDataFrame, VCFArray
Links To Me
Build Report  

Package Archives

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

Source Package SeqArray_1.25.3.tar.gz
Windows Binary SeqArray_1.25.3.zip
Mac OS X 10.11 (El Capitan) SeqArray_1.25.3.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

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