TreeSummarizedExperiment

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

TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

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DOI: 10.18129/B9.bioc.TreeSummarizedExperiment

Bioconductor version: Development (3.23)

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

Author: Ruizhu Huang [aut, cre] ORCID iD ORCID: 0000-0003-3285-1945 , Felix G.M. Ernst [ctb] ORCID iD ORCID: 0000-0001-5064-0928 , Mark Robinson [ctb] ORCID iD ORCID: 0000-0002-3048-5518 , Tuomas Borman [ctb] ORCID iD 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 "4.6") 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")

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 2.19.0

In Bioconductor since BioC 3.9 (R-3.6) (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

Suggests ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat

Linking To

Enhances

Depends On Me ExperimentSubset, HoloFoodR, MGnifyR, mia, miaSim, miaViz, curatedMetagenomicData, MicrobiomeBenchmarkData, microbiomeDataSets

Imports Me anansi, DspikeIn, iSEEtree, maaslin3, miaDash, miaTime, PLSDAbatch, treeclimbR, mikropml

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.

Source Package TreeSummarizedExperiment_2.19.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64) TreeSummarizedExperiment_2.19.0.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/

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