SeqArray
Data Management of Large-Scale Whole-Genome Sequence Variant Calls
Bioconductor version: Release (3.20)
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 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], David Levine [ctb], Cathy Laurie [ctb]
Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>
citation("SeqArray")):
Installation
To install this package, start R (version "4.4") 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 | 1.46.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), gdsfmt(>= 1.31.1) |
| Imports | methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors |
| System Requirements | |
| URL | https://github.com/zhengxwen/SeqArray |
| Bug Reports | https://github.com/zhengxwen/SeqArray/issues |
See More
| Suggests | Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation |
| Linking To | gdsfmt |
| Enhances | |
| Depends On Me | GBScleanR, SAIGEgds, SeqVarTools |
| Imports Me | GDSArray, GENESIS, ggmanh, VariantExperiment |
| Suggests Me | DelayedDataFrame, HIBAG, VCFArray, GMMAT, MAGEE |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SeqArray_1.46.0.tar.gz |
| Windows Binary (x86_64) | SeqArray_1.46.0.zip |
| macOS Binary (x86_64) | SeqArray_1.46.0.tgz |
| macOS Binary (arm64) | SeqArray_1.45.4.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 |