SeqArray

DOI: 10.18129/B9.bioc.SeqArray    

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

Bioconductor version: Release (3.8)

Big data management of 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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SeqArray", version = "3.8")

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 1.22.2
In Bioconductor since BioC 2.12 (R-3.0) (5.5 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 SeqVarTools
Imports Me GDSArray, GENESIS
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SeqArray_1.22.2.tar.gz
Windows Binary SeqArray_1.22.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) SeqArray_1.22.2.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 http://bioconductor.org/packages/SeqArray/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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