treeio
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see treeio.
Base Classes and Functions for Phylogenetic Tree Input and Output
Bioconductor version: 3.14
'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.
Author: Guangchuang Yu [aut, cre] 
, Tommy Tsan-Yuk Lam [ctb, ths], Shuangbin Xu [ctb] , Bradley Jones [ctb], Casey Dunn [ctb], Tyler Bradley [ctb], Konstantinos Geles [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("treeio")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("treeio")
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("treeio")| treeio | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software |
| Version | 1.18.1 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6.0) |
| Imports | ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.0), utils |
| System Requirements | |
| URL | https://github.com/YuLab-SMU/treeio(devel) https://docs.ropensci.org/treeio/(docs) https://yulab-smu.top/treedata-book/(book) https://doi.org/10.1093/molbev/msz240(paper) |
| Bug Reports | https://github.com/YuLab-SMU/treeio/issues |
See More
| Suggests | Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | ggtree, MicrobiotaProcess, TreeSummarizedExperiment |
| Suggests Me | enrichplot, ggtreeExtra, rfaRm |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | treeio_1.18.1.tar.gz |
| Windows Binary | treeio_1.18.1.zip |
| macOS 10.13 (High Sierra) | treeio_1.18.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/treeio |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/treeio |
| Bioc Package Browser | https://code.bioconductor.org/browse/treeio/ |
| Package Short Url | https://bioconductor.org/packages/treeio/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |