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>
citation("SeqArray")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SeqArray")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SeqArray")| R Integration | HTML | R Script |
| SeqArray Data Format and Access | HTML | R Script |
| SeqArray Overview | HTML | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Genetics, Infrastructure, Sequencing, Software |
| Version | 1.20.2 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), gdsfmt(>= 1.10.1) |
| Imports | methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors |
| System Requirements | |
| URL | http://github.com/zhengxwen/SeqArray |
| Bug Reports | http://github.com/zhengxwen/SeqArray/issues |
See More
| Suggests | digest, crayon, RUnit, knitr, Rcpp, SNPRelate, Biobase, BiocParallel, BiocGenerics, Rsamtools, VariantAnnotation |
| Linking To | gdsfmt |
| Enhances | |
| Depends On Me | SeqVarTools |
| Imports Me | GDSArray, GENESIS |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/SeqArray/ |
| Package Short Url | https://bioconductor.org/packages/SeqArray/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |