treeio

DOI: 10.18129/B9.bioc.treeio    

This is the development version of treeio; for the stable release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: Development (3.11)

'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]

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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, Software
Version 1.11.1
In Bioconductor since BioC 3.5 (R-3.4) (2.5 years)
License Artistic-2.0
Depends R (>= 3.4.0)
Imports ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.2.6), utils
LinkingTo
Suggests Biostrings, ggplot2, ggtree, igraph, knitr, phangorn, prettydoc, testthat, tidyr, vroom
SystemRequirements
Enhances
URL https://yulab-smu.github.io/treedata-book/
BugReports https://github.com/YuLab-SMU/treeio/issues
Depends On Me
Imports Me ggtree
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package treeio_1.11.1.tar.gz
Windows Binary treeio_1.11.1.zip
Mac OS X 10.11 (El Capitan) treeio_1.11.1.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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