DESCRIPTION

Package: rPHG2
Title: R interface to PHGv2
Version: 0.7.1
Authors@R:
    person(
        given = "Brandon",
        family = "Monier",
        email = "bm646@cornell.edu",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0001-6797-1221")
    )
Description:
    The aim of rPHG2 is to develop an R API for the practical haplotype
    graph version 2 (PHGv2). PHGv2 is the optimized successor to the PHG - a
    powerful tool for representing pangenomes. PHGv2 is optimized for plant
    breeding and genetics, where genomic diversity can be high, phased
    haplotypes are common (e.g. inbred lines), and imputation with low density
    markers is essential for breeding efficiency. This complements other
    imputation tools (e.g. BEAGLE) designed explicitly for handling samples
    from unphased species characterized by low genetic diversity and
    high-density genotyping.
License: Apache License (>= 2) | file LICENSE
URL:
    https://github.com/maize-genetics/rPHG2,
    https://rphg2.maizegenetics.net/
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: 
    R (>= 4.1.0)
Imports:
    cli,
    curl,
    GenomicRanges,
    GenomeInfoDb,
    ggplot2,
    httr,
    IRanges,
    jsonlite,
    methods,
    patchwork,
    rJava,
    rlang,
    S4Vectors,
    scales,
    tibble,
    tools,
    utils
VignetteBuilder: knitr
Suggests:
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3