treeio

DOI: 10.18129/B9.bioc.treeio  

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: Release (3.17)

'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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	treeio
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software
Version	1.24.3
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.9), utils, cli
LinkingTo
Suggests	Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr
SystemRequirements
Enhances
URL	https://github.com/YuLab-SMU/treeio(devel) https://docs.ropensci.org/treeio/(docs) https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/(book) https://doi.org/10.1093/molbev/msz240(paper)
BugReports	https://github.com/YuLab-SMU/treeio/issues
Depends On Me
Imports Me	geneplast.data, ggtree, MicrobiotaProcess, TreeSummarizedExperiment
Suggests Me	enrichplot, ggtreeDendro, ggtreeExtra, rfaRm
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	treeio_1.24.3.tar.gz
Windows Binary	treeio_1.24.3.zip
macOS Binary (x86_64)	treeio_1.24.3.tgz
macOS Binary (arm64)	treeio_1.24.3.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 3.17	Source Archive