TreeSummarizedExperiment
This is the development version of TreeSummarizedExperiment; for the stable release version, see TreeSummarizedExperiment.
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
Bioconductor version: Development (3.21)
TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.
Author: Ruizhu Huang [aut, cre] (ORCID:
Maintainer: Ruizhu Huang <ruizhuRH at gmail.com>
citation("TreeSummarizedExperiment")):
Installation
To install this package, start R (version "4.5") 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 |
Details
| biocViews | DataRepresentation, Infrastructure, Software |
| Version | 2.15.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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 | ExperimentSubset, HoloFoodR, MGnifyR, mia, miaSim, miaViz, curatedMetagenomicData, MicrobiomeBenchmarkData, microbiomeDataSets |
| Imports Me | iSEEtree, microSTASIS, PLSDAbatch, treeclimbR |
| Suggests Me | ANCOMBC, 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_2.15.0.tar.gz |
| Windows Binary (x86_64) | TreeSummarizedExperiment_2.15.0.zip |
| macOS Binary (x86_64) | TreeSummarizedExperiment_2.15.0.tgz |
| macOS Binary (arm64) | TreeSummarizedExperiment_2.15.0.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 |