TreeSummarizedExperiment

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Bioconductor version: Development (3.24)

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 , Mark Robinson [ctb] ORCID: 0000-0002-3048-5518 , Tuomas Borman [ctb] ORCID: 0000-0002-8563-8884

Maintainer: Ruizhu Huang <ruizhuRH at gmail.com>

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

Ruizhu Huang. TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures. doi:10.18129/B9.bioc.TreeSummarizedExperiment, R package version 2.21.0, https://bioconductor.org/packages/TreeSummarizedExperiment.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	2.21.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 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

Suggests	ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me	curatedMetagenomicData, ExperimentSubset, HoloFoodR, MGnifyR, mia, miaSim, miaViz, MicrobiomeBenchmarkData, microbiomeDataSets
Imports Me	anansi, benchdamic, CrcBiomeScreen, DspikeIn, iSEEtree, miaDash, miaTime, mikropml, treeclimbR
Suggests Me	ANCOMBC, dar, file2meco, hilldiv3, LegATo, LimROTS, maaslin3, microbiome, parafac4microbiome, philr, PLSDAbatch, radEmu
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	TreeSummarizedExperiment_2.21.0.tar.gz
Windows Binary (x86_64)	TreeSummarizedExperiment_2.21.0.zip
macOS Binary (big-sur-x86_64)	TreeSummarizedExperiment_2.21.0.tgz
macOS Binary (sonoma-arm64)	TreeSummarizedExperiment_2.21.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TreeSummarizedExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TreeSummarizedExperiment
Package Short Url	https://bioconductor.org/packages/TreeSummarizedExperiment/
Package Downloads Report	Download Stats