TreeSummarizedExperiment
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
Bioconductor version: Release (3.19)
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")
):
Installation
To install this package, start R (version "4.4") 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")
1. Introduction to TreeSE | HTML | R Script |
2. Combine TSEs | HTML | R Script |
Reference Manual |
Details
biocViews | DataRepresentation, Infrastructure, Software |
Version | 2.12.0 |
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, MGnifyR, mia, miaSim, miaViz, curatedMetagenomicData, MicrobiomeBenchmarkData, microbiomeDataSets |
Imports Me | ANCOMBC, benchdamic, CBEA, microSTASIS, PLSDAbatch, treeclimbR |
Suggests Me | dar, philr, file2meco |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | TreeSummarizedExperiment_2.12.0.tar.gz |
Windows Binary | TreeSummarizedExperiment_2.12.0.zip (64-bit only) |
macOS Binary (x86_64) | TreeSummarizedExperiment_2.12.0.tgz |
macOS Binary (arm64) | TreeSummarizedExperiment_2.12.0.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/ |
Package Downloads Report | Download Stats |