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TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Bioconductor version: Release (3.19)

TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.

Author: Ruizhu Huang [aut, cre] , Felix G.M. Ernst [ctb]

Maintainer: Ruizhu Huang <ruizhuRH at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Introduction to TreeSE HTML R Script
2. Combine TSEs HTML R Script
Reference Manual PDF


biocViews DataRepresentation, Infrastructure, Software
Version 2.12.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL (>=2)
Depends R (>= 3.6.0), SingleCellExperiment, S4Vectors(>= 0.23.18), Biostrings
Imports methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio
System Requirements
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Suggests ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
Linking To
Depends On Me ExperimentSubset, MGnifyR, mia, miaSim, miaViz, curatedMetagenomicData, MicrobiomeBenchmarkData, microbiomeDataSets
Imports Me ANCOMBC, benchdamic, CBEA, microSTASIS, PLSDAbatch, treeclimbR
Suggests Me dar, philr, file2meco
Links To Me
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Source Package TreeSummarizedExperiment_2.12.0.tar.gz
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macOS Binary (x86_64) TreeSummarizedExperiment_2.12.0.tgz
macOS Binary (arm64) TreeSummarizedExperiment_2.12.0.tgz
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Source Repository (Developer Access) git clone
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