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TreeSummarizedExperiment
This is thereleased version of TreeSummarizedExperiment; for the devel version, seeTreeSummarizedExperiment.
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
Bioconductor version: Release (3.22)
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("TreeSummarizedExperiment")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("TreeSummarizedExperiment")For older versions of R, please refer to the appropriateBioconductor 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 | 2.18.0 |
| 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 |
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 | 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
FollowInstallation instructions to use this package in your R session.
| Source Package | TreeSummarizedExperiment_2.18.0.tar.gz |
| Windows Binary (x86_64) | TreeSummarizedExperiment_2.18.0.zip |
| macOS Binary (x86_64) | TreeSummarizedExperiment_2.18.0.tgz |
| macOS Binary (arm64) | TreeSummarizedExperiment_2.18.0.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 |
| Old Source Packages for BioC 3.22 | Source Archive |