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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: 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")
| SeqArray-JSM2013.pdf | ||
| HTML | A Brief Introduction to Data Analytics on SeqArray GDS Files | |
| HTML | SeqArray – Big Data Management of Genome-Wide Sequence Variants | |
| 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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