treeio

DOI: 10.18129/B9.bioc.treeio    

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: Release (3.12)

'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], Casey Dunn [ctb], Bradley Jones [ctb], Tyler Bradley [ctb], Shuangbin Xu [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 "4.0") and enter:

if (!requireNamespace("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 1.14.0
In Bioconductor since BioC 3.5 (R-3.4) (3.5 years)
License Artistic-2.0
Depends R (>= 3.6.0)
Imports ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.0), utils
LinkingTo
Suggests Biostrings, ggplot2, ggtree, igraph, knitr, phangorn, prettydoc, testthat, tidyr, vroom, xml2
SystemRequirements
Enhances
URL https://github.com/YuLab-SMU/treeio(devel) https://docs.ropensci.org/treeio/(docs) https://yulab-smu.top/treedata-book/(book)
BugReports https://github.com/YuLab-SMU/treeio/issues
Depends On Me
Imports Me ggtree
Suggests Me ggtreeExtra, MicrobiotaProcess, rfaRm
Links To Me
Build Report  

Package Archives

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

Source Package treeio_1.14.0.tar.gz
Windows Binary treeio_1.13.1.zip
macOS 10.13 (High Sierra) treeio_1.14.0.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

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