DESCRIPTION

Package: rPHG
Version: 0.2.3
Date: 2019-06-03
Title: R front-end for the practical haplotype graph
Authors@R: c(
    person(
        given = "Brandon",
        family = "Monier",
        email = "brandon.monier@gmail.com",
        role = c("aut", "cre")
    ),
    person(
        given = "Peter",
        family = "Bradbury",
        role = c("aut")
    ),
    person(
        given = "Terry",
        family = "Casstevens",
        role = c("aut")
    ),
    person(
        given = "Jean-Luc",
        family = "Jannink",
        role = c("aut")
    ),
    person(
        given = "Ed",
        family = "Buckler",
        email = "esb33@cornell.edu",
        role = c("aut")
    ))
Description:
    The aim of rPHG is to develop an R API for the practical haplotype
    graph (PHG). The PHG is a trellis graph based representation of genic and
    intergenic regions (called reference ranges or reference intervals) which
    represent diversity across and between taxa. It can be used to: create
    custom genomes for alignment, call rare alleles, impute genotypes, and
    efficiently store genomic data from many lines (i.e. reference, assemblies,
    and other lines). Skim sequences generated for a given taxon are aligned
    to consensus sequences in the PHG to identify the haplotype node at a
    given anchor. All the anchors for a given taxon are processed through a
    Hidden Markov Model (HMM) to identify the most likely path through the
    graph. Path information is used to identify the variants (SNPs). Low cost
    sequencing technologies, coupled with the PHG, facilitate the genotyping
    of large number of samples to increase the size of training populations
    for genomic selection models. This can in turn increase predictive accuracy
    and selection intensity in a breeding program.
License: Apache License (>= 2) | file LICENSE
URL: https://github.com/maize-genetics/rPHG,
    https://rphg.maizegenetics.net/
Imports:
    cli,
    curl,
    GenomicRanges,
    ggplot2,
    httr,
    IRanges,
    jsonlite,
    methods,
    rJava,
    rlang,
    tibble,
    visNetwork
Depends:
    SummarizedExperiment
Suggests:
    BiocStyle,
    knitr,
    testthat
Encoding: UTF-8
LazyData: true
VignetteBuilder:
    knitr
RoxygenNote: 7.3.1
biocViews:
    GenomeWideAssociation