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 Whole-genome Sequence Variant Calls

Bioconductor version: Release (3.3)

Big data management of whole-genome sequence variant calls with thousands of individuals: genotypic data (e.g., SNVs, 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

HTML R Script SeqArray Data Analytics
HTML R Script SeqArray Data Format and Access
HTML SeqArray Overview
PDF   Reference Manual
Text   NEWS

Details

biocViews Genetics, Infrastructure, Sequencing, Software
Version 1.12.5
In Bioconductor since BioC 2.12 (R-3.0) (3 years)
License GPL-3
Depends R (>= 3.3.0), gdsfmt(>= 1.8.0)
Imports methods, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VariantAnnotation
LinkingTo gdsfmt
Suggests parallel, digest, crayon, 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 GENESIS
Build Report  

Package Archives

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

Package Source SeqArray_1.12.5.tar.gz
Windows Binary SeqArray_1.12.5.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) SeqArray_1.12.5.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SeqArray/tree/release-3.3
Package Short Url http://bioconductor.org/packages/SeqArray/
Package Downloads Report Download Stats

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