DESCRIPTION

Package: colockit
Type: Package
Title: A Toolkit for Colocalisation Analysis
Version: 0.1.0
Authors@R: person("Andrii Iakovliev", role = c("aut", "cre"),
                  email = "a.iakovliev@icloud.com")
Author: Andrii Iakovliev [aut, cre]
Maintainer: Andrii Iakovliev <a.iakovliev@icloud.com>
Description: Provides a two-stage pipeline for genomic colocalisation
    analysis. In the first stage, GWAS summary statistics for two traits are
    harmonised, allele frequencies are validated, and a linkage disequilibrium
    matrix is computed for the region of interest. In the second stage, the
    prepared data are passed to one of several supported colocalisation methods.
    Two backends are available: a standalone backend that accepts user-supplied
    summary statistics and LD matrices without any external database dependency,
    and a genoscores backend that integrates with the Genoscores database and
    infrastructure for published and private GWAS. Currently supported methods
    are coloc ABF, coloc SuSiE, and PWCoCo, with placeholders for additional
    methods in future releases.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends:
    R (>= 4.1.0)
Imports:
    data.table (>= 1.14.0),
    coloc (>= 5.1.0),
    bigsnpr (>= 1.12.0),
    ggplot2 (>= 3.4.0),
    ggrepel (>= 0.9.0),
    gridExtra (>= 2.3),
    LDheatmap (>= 1.0.0),
    grDevices,
    stats
Suggests:
    DBI,
    genoscores,
    knitr,
    pkgload,
    rcmdcheck,
    rmarkdown,
    roxygen2,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3