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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
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Big Data Management of Whole-genome Sequence Variant Calls
Bioconductor version: Release (3.4)
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 | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataRepresentation, Genetics, Infrastructure, Sequencing, Software |
| Version | 1.14.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 3.3.0), gdsfmt(>= 1.10.1) |
| Imports | methods, parallel, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, SummarizedExperiment, Biostrings, VariantAnnotation |
| LinkingTo | gdsfmt |
| Suggests | BiocParallel, digest, crayon, RUnit, Biobase, 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 | GENESIS |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SeqArray_1.14.1.tar.gz |
| Windows Binary | SeqArray_1.14.1.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | SeqArray_1.14.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SeqArray/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/SeqArray/ |
| Package Downloads Report | Download Stats |
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