Package: HaploVar
Type: Package
Title: Defining Local Haplotype Variants for Use in Trait Association
        and Trait Prediction Analyses
Version: 0.1.1
Authors@R: c(person("Tessa", "MacNish", email = "tessa.macnish@research.uwa.edu.au", role = c("aut", "cre"), comment = c(ORCID = "0009-0008-8985-7348")), person("Hawlader", "Al-Mamun", role = "ctb"), person("Thomas", "Bergmann", role = "ctb"), person("Mitchell", "Bestry", role = "ctb"), person("Jacob", "Marsh", role = "ctb"), person("David", "Edwards", role = "ctb"))
Description: A local haplotyping tool for use in trait association and
        trait prediction analyses pipelines. 'HaploVar' enables users
        take single nucleotide polymorphisms (SNPs) (in VCF format) and
        a linkage disequilibrium (LD) matrix, calculate local
        haplotypes and format the output to be compatible with a wide
        range of trait association and trait prediction tools. The
        local haplotypes are calculated from the LD matrix using a
        clustering algorithm called density-based spatial clustering of
        applications with noise ('DBSCAN') (Ester et al., 1996) <ISBN:
        1577350049>.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: dplyr, tidyr, tibble, magrittr, dbscan
Depends: R (>= 4.00)
LazyData: true
LazyDataCompression: xz
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-06-17 10:48:04 UTC; root
Author: Tessa MacNish [aut, cre] (ORCID:
        <https://orcid.org/0009-0008-8985-7348>), Hawlader Al-Mamun
        [ctb], Thomas Bergmann [ctb], Mitchell Bestry [ctb], Jacob
        Marsh [ctb], David Edwards [ctb]
Maintainer: Tessa MacNish <tessa.macnish@research.uwa.edu.au>
Config/pak/sysreqs: libicu-dev
Repository: https://t-macnish.r-universe.dev
Date/Publication: 2025-07-21 08:31:11 UTC
RemoteUrl: https://github.com/cran/HaploVar
RemoteRef: HEAD
RemoteSha: 7402a12912cb4ebd15ba168e748b2eb3c1f30722