TreeSummarizedExperiment
TreeSummarizedExperiment: a S4 Class for Data with Tree Structures
Bioconductor version: 3.24 · Package version: 2.21.0
TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TreeSummarizedExperiment")Details
| Maintainer | Ruizhu Huang <ruizhuRH@gmail.com> |
| Author | Ruizhu Huang [aut, cre] (ORCID: <https://orcid.org/0000-0003-3285-1945>), Felix G.M. Ernst [ctb] (ORCID: <https://orcid.org/0000-0001-5064-0928>), Mark Robinson [ctb] (ORCID: <https://orcid.org/0000-0002-3048-5518>), Tuomas Borman [ctb] (ORCID: <https://orcid.org/0000-0002-8563-8884>) |
| License | GPL (>=2) |
| Downloads rank | 3117 |
| Source branch | devel |
| biocViews | DataRepresentation, Infrastructure, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | TreeSummarizedExperiment_2.21.0.tar.gz |
| Windows binary (x86_64) | TreeSummarizedExperiment_2.21.0.zip |
| macOS binary (arm64) | TreeSummarizedExperiment_2.21.0.tgz |
| macOS binary (x86_64) | TreeSummarizedExperiment_2.21.0.tgz |
Dependencies
Depends: R (>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings
Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio
Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
Reverse dependencies
Depends On Me (9): curatedMetagenomicData, ExperimentSubset, HoloFoodR, MGnifyR, mia, miaSim, miaViz, MicrobiomeBenchmarkData, microbiomeDataSets
Imports Me (9): anansi, benchdamic, CrcBiomeScreen, DspikeIn, iSEEtree, miaDash, miaTime, mikropml, treeclimbR
Suggests Me (11): ANCOMBC, dar, file2meco, LegATo, LimROTS, maaslin3, microbiome, parafac4microbiome, philr, PLSDAbatch, radEmu