Package: GDSAnnotator
Type: Package
Title: Whole-genome variant annotation data manipulation using GDS
        files
Version: 0.99.1
Depends: R (>= 4.5.0), 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
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-27 03:30:01 UTC
RemoteUrl: https://github.com/BiocStaging/GDSAnnotator
RemoteRef: HEAD
RemoteSha: f37e87d74b0a005e2b8d261fe533927fdd8ea359
NeedsCompilation: no
Packaged: 2026-09-27 08:29:14 UTC; root
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>