Package: treeclimbR
Type: Package
Title: An algorithm to find optimal signal levels in a tree
Version: 1.9.0
Date: 2025-07-18
Authors@R: c(person("Ruizhu", "Huang", email = "ruizhuRH@gmail.com",
                    role = c("aut"), 
                    comment = c(ORCID = "0000-0003-3285-1945")),
             person("Charlotte", "Soneson", 
                    email = "charlottesoneson@gmail.com",
                    role = c("aut", "cre"), 
                    comment = c(ORCID = "0000-0003-3833-2169")))
Description: The arrangement of hypotheses in a hierarchical structure
        appears in many research fields and often indicates different
        resolutions at which data can be viewed. This raises the
        question of which resolution level the signal should best be
        interpreted on. treeclimbR provides a flexible method to select
        optimal resolution levels (potentially different levels in
        different parts of the tree), rather than cutting the tree at
        an arbitrary level. treeclimbR uses a tuning parameter to
        generate candidate resolutions and from these selects the
        optimal one.
License: Artistic-2.0
Encoding: UTF-8
biocViews: StatisticalMethod, CellBasedAssays
Depends: R (>= 4.4.0)
Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods,
        SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr,
        ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree,
        stats, utils, rlang
Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle,
        GenomeInfoDb
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/csoneson/treeclimbR
BugReports: https://github.com/csoneson/treeclimbR/issues
Config/testthat/edition: 3
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:02:33 UTC
RemoteUrl: https://github.com/bioc/treeclimbR
RemoteRef: HEAD
RemoteSha: 90a98f4232fb5577b10d9a181750d1909a1aaf48
NeedsCompilation: no
Packaged: 2026-06-06 06:11:47 UTC; root
Author: Ruizhu Huang [aut] (ORCID: <https://orcid.org/0000-0003-3285-1945>),
  Charlotte Soneson [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3833-2169>)
Maintainer: Charlotte Soneson <charlottesoneson@gmail.com>