Package: GDSAnnotator
Type: Package
Title: Whole-genome variant annotation data manipulation using GDS
        files
Version: 0.99.2
Depends: R (>= 4.6.0), gdsfmt (>= 1.32.0), SeqArray (>= 1.53.2)
Imports: methods, utils, IRanges, GenomicRanges, S4Vectors
Suggests: VariantAnnotation, BiocStyle, knitr, rmarkdown, testthat (>=
        3.0.0)
Authors@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre"),
        email="xiuwen.zheng@abbvie.com",
        comment=c(ORCID="0000-0002-1390-0708")),
        person("Yuantao (Raven)", "Chen", role="ctb"),
        person("Hufeng", "Zhou", role="ctb", email="hufengzhou@g.harvard.edu"))
Description: Fast and memory-efficient manipulation of whole-genome variant
        annotation data stored in Genomic Data Structure (GDS) files. The
        annotated GDS (aGDS) format introduced by FAVOR stores the FAVOR
        annotations of the variants together with the genotypes in one SeqArray
        GDS file. This package generalizes the format to annotation GDS files of
        any source, with or without genotypes. Annotation resources and
        annotator outputs, including FAVOR, gnomAD, Ensembl VEP and SnpEff, are
        converted into compact SeqArray-compatible GDS files with random access.
        Variants can be given as chr-pos-ref-alt strings, data frames, GRanges
        objects, VCF files or objects, or SeqArray GDS files. They are annotated
        by querying the annotation files, and the annotations can be written
        back into a genotype GDS file. Summary statistics of the variants and
        their annotations are computed in a single pass over a file and rendered
        as a VEP/SnpEff-like report. The package is intended for large-scale
        whole-genome sequencing studies.
License: GPL-3
URL: https://github.com/zhengxwen/GDSAnnotator
BugReports: https://github.com/zhengxwen/GDSAnnotator/issues
VignetteBuilder: knitr
Encoding: UTF-8
ByteCompile: TRUE
biocViews: Infrastructure, DataRepresentation, DataImport, Sequencing,
        WholeGenome, Genetics, Annotation, VariantAnnotation,
        GenomeAnnotation, GenomicVariation
git_url: https://git.bioconductor.org/packages/GDSAnnotator
git_branch: devel
git_last_commit: 40f9a3d
git_last_commit_date: 2026-10-18
Repository: Bioconductor 3.24
Date/Publication: 2026-10-23
NeedsCompilation: no
Packaged: 2026-10-23 21:49:44 UTC; biocbuild
Author: Xiuwen Zheng [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1390-0708>),
  Yuantao (Raven) Chen [ctb],
  Hufeng Zhou [ctb]
Maintainer: Xiuwen Zheng <xiuwen.zheng@abbvie.com>
Built: R 4.6.1; ; 2026-10-24 12:38:58 UTC; unix
