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TreeSummarizedExperiment

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 gmail.com>

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

Installation

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


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

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

Details

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
URL
See More
Suggests ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me curatedMetagenomicData, ExperimentSubset, MGnifyR, mia, miaSim, miaViz, MicrobiomeBenchmarkData, microbiomeDataSets
Imports Me ANCOMBC, benchdamic, CBEA, microSTASIS, PLSDAbatch, treeclimbR
Suggests Me dar, philr
Links To Me
Build Report Build Report

Package Archives

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

Source Package TreeSummarizedExperiment_2.12.0.tar.gz
Windows Binary TreeSummarizedExperiment_2.12.0.zip
macOS Binary (x86_64) TreeSummarizedExperiment_2.12.0.tgz
macOS Binary (arm64) TreeSummarizedExperiment_2.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TreeSummarizedExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TreeSummarizedExperiment
Bioc Package Browser https://code.bioconductor.org/browse/TreeSummarizedExperiment/
Package Short Url https://bioconductor.org/packages/TreeSummarizedExperiment/
Package Downloads Report Download Stats