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An algorithm to find optimal signal levels in a tree

Bioconductor version: Release (3.19)

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.

Author: Ruizhu Huang [aut] , Charlotte Soneson [aut, cre]

Maintainer: Charlotte Soneson <charlottesoneson at>

Citation (from within R, enter citation("treeclimbR")):


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Reference Manual PDF


biocViews CellBasedAssays, Software, StatisticalMethod
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
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
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Source Package treeclimbR_1.0.0.tar.gz
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