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>

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

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.

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

Version 2.6.0

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

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

Linking To

Enhances

Imports Me ANCOMBC, benchdamic, CBEA

Suggests Me philr

Links To Me

Build Report Build Report

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

Source Repository git clone https://git.bioconductor.org/packages/TreeSummarizedExperiment

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TreeSummarizedExperiment

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Old Source Packages for BioC 3.16 Source Archive