TreeSummarizedExperiment

DOI: 10.18129/B9.bioc.TreeSummarizedExperiment  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TreeSummarizedExperiment.

TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	2.6.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 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
LinkingTo
Suggests	ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me	curatedMetagenomicData, ExperimentSubset, mia, miaSim, miaViz, MicrobiomeBenchmarkData, microbiomeDataSets
Imports Me	ANCOMBC, benchdamic, CBEA
Suggests Me	philr
Links To Me
Build Report

Package Archives

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

Source Package	TreeSummarizedExperiment_2.6.0.tar.gz
Windows Binary	TreeSummarizedExperiment_2.6.0.zip
macOS Binary (x86_64)	TreeSummarizedExperiment_2.6.0.tgz
macOS Binary (arm64)	TreeSummarizedExperiment_2.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TreeSummarizedExperiment
Source Repository (Developer Access)	git clone [email protected]:packages/TreeSummarizedExperiment
Bioc Package Browser	https://code.bioconductor.org/browse/TreeSummarizedExperiment/
Package Short Url	https://bioconductor.org/packages/TreeSummarizedExperiment/
Package Downloads Report	Download Stats