To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SeqArray")

In most cases, you don't need to download the package archive at all.

SeqArray

 

   

Big Data Management of Genome-Wide Sequence Variants

Bioconductor version: Release (3.2)

Big data management of genome-wide sequence variants with thousands of individuals: genotypic data (e.g., SNPs, indels and structural variation calls) and annotations in 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], 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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SeqArray")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SeqArray")

 

PDF SeqArray-JSM2013.pdf
HTML A Brief Introduction to Data Analytics on SeqArray GDS Files
HTML SeqArray – Big Data Management of Genome-Wide Sequence Variants
PDF   Reference Manual
Text   NEWS

Details

biocViews Genetics, Infrastructure, Sequencing, Software
Version 1.10.6
In Bioconductor since BioC 2.12 (R-3.0) (3 years)
License GPL-3
Depends gdsfmt(>= 1.6.2)
Imports methods, Biostrings, GenomicRanges, IRanges, S4Vectors, VariantAnnotation, SummarizedExperiment
LinkingTo gdsfmt
Suggests parallel, RUnit, BiocGenerics, knitr, Rcpp, SNPRelate
SystemRequirements
Enhances
URL http://github.com/zhengxwen/SeqArray
BugReports http://github.com/zhengxwen/SeqArray/issues
Depends On Me SeqVarTools
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source SeqArray_1.10.6.tar.gz
Windows Binary SeqArray_1.10.6.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SeqArray_1.10.3.tgz
Mac OS X 10.9 (Mavericks) SeqArray_1.10.6.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SeqArray/tree/release-3.2
Package Short Url http://bioconductor.org/packages/SeqArray/
Package Downloads Report Download Stats

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