SeqArray
Data management of large-scale whole-genome sequence variant calls using GDS files
Bioconductor version: 3.24 · Package version: 1.53.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SeqArray")Details
| Maintainer | Xiuwen Zheng <zhengx@u.washington.edu> |
| Author | Xiuwen Zheng [aut, cre] (ORCID: <https://orcid.org/0000-0002-1390-0708>), Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb] |
| License | GPL-3 |
| URL | https://github.com/zhengxwen/SeqArray |
| Bug Reports | https://github.com/zhengxwen/SeqArray/issues |
| System Requirements | zlib: zlib1g-dev (deb), zlib-devel (rpm) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, Genetics, Infrastructure, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/SeqArray/ |
Citation
From within R, enter citation("SeqArray"):
Xiuwen Zheng, Stephanie Gogarten. SeqArray: Data management of large-scale whole-genome sequence variant calls using GDS files. doi:10.18129/B9.bioc.SeqArray, R package version 1.53.3, https://bioconductor.org/packages/SeqArray.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SeqArray_1.53.3.tar.gz |
| Windows binary (x86_64) | SeqArray_1.53.3.zip |
| macOS binary (arm64) | SeqArray_1.53.3.tgz |
| macOS binary (x86_64) | SeqArray_1.53.3.tgz |
Dependencies
Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1)
Imports: methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, Seqinfo, Biostrings
LinkingTo: gdsfmt
Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, crayon, knitr, markdown, rmarkdown, VariantAnnotation
Reverse dependencies
Depends On Me (3): GBScleanR, SAIGEgds, SeqVarTools
Imports Me (5): GDSArray, GENESIS, ggmanh, pgen2gds, VariantExperiment
Suggests Me (6): DelayedDataFrame, gdscloud, GMMAT, HIBAG, MAGEE, VCFArray