treeio

DOI: 10.18129/B9.bioc.treeio    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: 3.15

'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 "4.2") 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	1.20.2
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.9), utils
LinkingTo
Suggests	Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml
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	ggtree, MicrobiotaProcess, TreeSummarizedExperiment
Suggests Me	enrichplot, ggtreeExtra, rfaRm
Links To Me
Build Report

Package Archives

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

Source Package	treeio_1.20.2.tar.gz
Windows Binary	treeio_1.20.2.zip
macOS Binary (x86_64)	treeio_1.20.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/treeio
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/treeio
Package Short Url	https://bioconductor.org/packages/treeio/
Package Downloads Report	Download Stats