DOI: 10.18129/B9.bioc.SeqArray  

Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Bioconductor version: Release (3.17)

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>

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HTML R Script R Integration
HTML R Script SeqArray Data Format and Access
HTML SeqArray Overview
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biocViews DataRepresentation, Genetics, Infrastructure, Sequencing, Software
Version 1.40.1
In Bioconductor since BioC 2.12 (R-3.0) (10.5 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.31.1)
Imports methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
LinkingTo gdsfmt
Suggests Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation
Depends On Me GBScleanR, SAIGEgds, SeqVarTools
Imports Me GDSArray, GENESIS, ggmanh, VariantExperiment
Suggests Me DelayedDataFrame, HIBAG, VCFArray
Links To Me
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