SeqArray

DOI: 10.18129/B9.bioc.SeqArray    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see SeqArray.

Big Data Management of Whole-genome Sequence Variant Calls

Bioconductor version: 3.7

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>

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")

 

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	1.20.2
In Bioconductor since	BioC 2.12 (R-3.0) (5.5 years)
License	GPL-3
Depends	R (>= 3.5.0), gdsfmt(>= 1.10.1)
Imports	methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
LinkingTo	gdsfmt
Suggests	digest, crayon, RUnit, knitr, Rcpp, SNPRelate, Biobase, BiocParallel, BiocGenerics, 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_1.20.2.tar.gz
Windows Binary	SeqArray_1.20.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	SeqArray_1.20.2.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