Package: phylogenize
Title: Associate Microbial Prevalence, Specificity, and Abundance with
        Gene Presence
Version: 2.0.0.0001
Authors@R: 
    c(person(given = "Patrick",
           family = "Bradley",
           role = c("aut", "cre"),
           email = "bradley.720@osu.edu"),
     person(given = "Kathryn",
           family = "Kananen",
           role = c("aut"),
           email = "kananen.13@osu.edu"))     
Description: phylogenize contains functions to estimate microbial prevalence and specificity scores from data, to associate these quantitative phenotypes with gene presence/absence (using the implementation of phylogenetic regression from the package phylolm), and to visualize the results. Both shotgun metagenomics and 16S amplicon data can be used with this pipeline.
License: MIT
Encoding: UTF-8
LazyData: true
Depends: readr, dplyr, stringr, tidyr, tibble, purrr, Matrix
Imports: ape, ashr, biomformat, castor, crosstalk, dplyr, DT,
        extraDistr, forcats, ggplot2, ggtree, graphics, grDevices,
        htmlwidgets, kableExtra, knitr, MASS, Matrix, methods,
        parallel, patchwork, pbapply, phylolm, plotly, purrr, qvalue,
        readr, rlang, rmarkdown, S4Vectors, scales, seqinr, settings,
        stats, stringr, svglite, tibble, tidyr, yaml
Suggests: ANCOMBC, Maaslin2, POMS, clusterProfiler
RoxygenNote: 7.3.2
Author: Patrick Bradley [aut, cre],
  Kathryn Kananen [aut]
Maintainer: Patrick Bradley <bradley.720@osu.edu>
Built: R 4.1.3; ; 2025-06-06 03:11:13 UTC; unix
