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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/TreeSummarizedExperiment.html below:

Bioconductor - TreeSummarizedExperiment (development version)

TreeSummarizedExperiment

This is the development version of TreeSummarizedExperiment; for the stable release version, see TreeSummarizedExperiment.

TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Bioconductor version: Development (3.22)

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

Author: Ruizhu Huang [aut, cre] ORCID: 0000-0003-3285-1945 , Felix G.M. Ernst [ctb] ORCID: 0000-0001-5064-0928 , Tuomas Borman [ctb] ORCID: 0000-0002-8563-8884

Maintainer: Ruizhu Huang <ruizhuRH at gmail.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TreeSummarizedExperiment")

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

Documentation

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

browseVignettes("TreeSummarizedExperiment")
Details biocViews DataRepresentation, Infrastructure, Software Version 2.17.0 In Bioconductor since BioC 3.9 (R-3.6) (6 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 URL See More Suggests ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat Linking To Enhances Depends On Me ExperimentSubset, HoloFoodR, MGnifyR, mia, miaSim, miaViz, curatedMetagenomicData, MicrobiomeBenchmarkData, microbiomeDataSets Imports Me iSEEtree, maaslin3, miaDash, microSTASIS, PLSDAbatch, treeclimbR Suggests Me ANCOMBC, dar, philr, LegATo, file2meco, parafac4microbiome Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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