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

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see SeqArray.

Big Data Management of Whole-genome Sequence Variant Calls

Bioconductor version: 3.3

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 <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	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	1.12.9
In Bioconductor since	BioC 2.12 (R-3.0) (3.5 years)
License	GPL-3
Depends	R (>= 3.3.0), gdsfmt(>= 1.8.0)
Imports	methods, parallel, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, SummarizedExperiment, Biostrings, VariantAnnotation
LinkingTo	gdsfmt
Suggests	BiocParallel, digest, crayon, RUnit, Biobase, BiocGenerics, knitr, Rcpp, SNPRelate, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL	http://github.com/zhengxwen/SeqArray
BugReports	http://github.com/zhengxwen/SeqArray/issues
Depends On Me	SeqVarTools
Imports Me	GENESIS
Suggests Me
Build Report

Package Archives

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

Package Source	SeqArray_1.12.9.tar.gz
Windows Binary	SeqArray_1.12.9.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks)	SeqArray_1.12.9.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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