Package: clusnalyst
Title: Point-and-Click Cluster Analysis of Molecular and Trait Data
Version: 0.1.0
Authors@R: c(
    person("Ebenezer", "Ogoe", , "ebenezerogoe@gmail.com", role = c("aut", "cre", "cph"),
           comment = "Co-creator; wrote the 2026 package"),
    person("Michael", "Obeng", role = "aut",
           comment = "Co-creator of Clusnalyst (2022)"),
    person("Stephen", "Amoako", role = "aut",
           comment = "Co-creator of Clusnalyst (2022)")
  )
Description: A 'shiny' application and a set of plain R functions for
        clustering samples from dominant markers, SNP genotypes (CSV,
        VCF or HapMap), quantitative or mixed traits, and DNA or
        protein sequences. It computes distance matrices, builds trees
        by UPGMA, WPGMA, single, complete or Ward linkage, neighbour
        joining or BIONJ, and checks them with marker bootstrap support
        (Felsenstein 1985 <doi:10.1111/j.1558-5646.1985.tb00420.x>),
        cophenetic correlation, average silhouette width, the gap
        statistic and Mantel tests. It also offers principal
        coordinates and principal components, k-means and partitioning
        around medoids, and exports a self-contained HTML report and an
        R script that reproduces the analysis.
License: MIT + file LICENSE
URL: https://github.com/ebenogoe/clusnalyst,
        https://ebenogoe.github.io/clusnalyst/
BugReports: https://github.com/ebenogoe/clusnalyst/issues
Depends: R (>= 4.1.0)
Imports: ade4, ape, Biostrings, bsicons, bslib (>= 0.8.0), cicerone,
        cluster, config, ggiraph, ggplot2 (>= 3.5.0), ggtree, golem,
        grDevices, htmltools, jsonlite, methods, msa, reactable,
        readxl, seqinr, shiny (>= 1.8.1), stats, svglite, tools, utils,
        vcfR, writexl
Suggests: chromote, pkgload, shinytest2, testthat (>= 3.0.0)
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-GB
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev make libharfbuzz-dev libicu-dev
        libpng-dev libuv1-dev zlib1g-dev
Repository: https://ebenogoe.r-universe.dev
Date/Publication: 2026-10-14 19:33:12 UTC
RemoteUrl: https://github.com/ebenogoe/clusnalyst
RemoteRef: main
RemoteSha: 026a65b73d10f5831353ea0330258c363a2299d5
NeedsCompilation: no
Packaged: 2026-10-14 22:33:28 UTC; root
Author: Ebenezer Ogoe [aut, cre, cph] (Co-creator; wrote the 2026 package),
  Michael Obeng [aut] (Co-creator of Clusnalyst (2022)),
  Stephen Amoako [aut] (Co-creator of Clusnalyst (2022))
Maintainer: Ebenezer Ogoe <ebenezerogoe@gmail.com>