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Showing content from http://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/SeqArray.html below:

Bioconductor - SeqArray (development version)

SeqArray

This is the development version of SeqArray; for the stable release version, see SeqArray.

Data management of large-scale whole-genome sequence variant calls using GDS files

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-1390-0708 , Stephanie Gogarten [aut], David Levine [ctb], Cathy Laurie [ctb]

Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>

Citation (from within R, enter citation("SeqArray")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews DataRepresentation, Genetics, Infrastructure, Sequencing, Software Version 1.49.3 In Bioconductor since BioC 2.12 (R-3.0) (12.5 years) License GPL-3 Depends R (>= 3.5.0), gdsfmt(>= 1.31.1) Imports methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, 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 Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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