SeqArray
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SeqArray.
Data Management of Large-scale Whole-genome Sequence Variant Calls
Bioconductor version: 3.9
Data management of large-scale 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 <zhengxwen at gmail.com>
citation("SeqArray")
):
Installation
To install this package, start R (version "3.6") 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 | 1.24.2 |
In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
License | GPL-3 |
Depends | R (>= 3.5.0), gdsfmt(>= 1.18.0) |
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 | Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation |
Linking To | gdsfmt |
Enhances | |
Depends On Me | SeqVarTools |
Imports Me | GDSArray, GENESIS |
Suggests Me | DelayedDataFrame, VCFArray |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | SeqArray_1.24.2.tar.gz |
Windows Binary | SeqArray_1.24.2.zip |
Mac OS X 10.11 (El Capitan) | SeqArray_1.24.2.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 3.9 | Source Archive |