SeqArray: Big Data Management of Genome-Wide Sequence Variants

GNU General Public License, GPLv3

Features

Big data management of genome-wide sequence variants with thousands of individuals: genotypic data (e.g., SNP, indel 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.

Bioconductor:

Release Version: v1.10.1

http://www.bioconductor.org/packages/release/bioc/html/SeqArray.html

• Tutorials: Data Management, Data Analytics

Development Version: v1.11.0

http://www.bioconductor.org/packages/devel/bioc/html/SeqArray.html

• Tutorials: Data Management, Data Analytics

Installation

• Bioconductor repository:

source("http://bioconductor.org/biocLite.R")
biocLite("SeqArray")

• Development version from Github:

library("devtools")
install_github("zhengxwen/gdsfmt")
install_github("zhengxwen/SeqArray")

The install_github() approach requires that you build from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

• Install the package from the source code:

gdsfmt, SeqArray

wget --no-check-certificate https://github.com/zhengxwen/gdsfmt/tarball/master -O gdsfmt_latest.tar.gz
wget --no-check-certificate https://github.com/zhengxwen/SeqArray/tarball/master -O SeqArray_latest.tar.gz
R CMD INSTALL gdsfmt_latest.tar.gz
R CMD INSTALL SeqArray_latest.tar.gz

## Or
curl -L https://github.com/zhengxwen/gdsfmt/tarball/master/ -o gdsfmt_latest.tar.gz
curl -L https://github.com/zhengxwen/SeqArray/tarball/master/ -o SeqArray_latest.tar.gz
R CMD INSTALL gdsfmt_latest.tar.gz
R CMD INSTALL SeqArray_latest.tar.gz