treeio

DOI: 10.18129/B9.bioc.treeio    

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: Release (3.16)

'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 (from within R, enter citation("treeio")):

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 1.22.0
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, 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 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_1.22.0.tar.gz
Windows Binary treeio_1.22.0.zip
macOS Binary (x86_64) treeio_1.22.0.tgz
macOS Binary (arm64) treeio_1.22.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: