SeqArray
This is the released version of SeqArray; for the devel version, see SeqArray.
Data management of large-scale whole-genome sequence variant calls using GDS files
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.52.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), gdsfmt(>= 1.31.1) |
| Imports | methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, Seqinfo, Biostrings |
| 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, 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_1.52.1.tar.gz |
| Windows Binary (x86_64) | SeqArray_1.52.1.zip |
| macOS Binary (big-sur-x86_64) | SeqArray_1.52.1.tgz |
| macOS Binary (sonoma-arm64) | SeqArray_1.52.1.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 3.23 | Source Archive |