treeio
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see treeio.
Base Classes and Functions for Phylogenetic Tree Input and Output
Bioconductor version: 3.11
'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("treeio")
):
Installation
To install this package, start R (version "4.0") 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")
treeio | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Software |
Version | 1.12.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
License | Artistic-2.0 |
Depends | R (>= 3.4.0) |
Imports | ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.2.6), utils |
System Requirements | |
URL | https://github.com/YuLab-SMU/treeio(devel) https://docs.ropensci.org/treeio/(docs) https://yulab-smu.github.io/treedata-book/(book) |
Bug Reports | https://github.com/YuLab-SMU/treeio/issues |
See More
Suggests | Biostrings, ggplot2, ggtree, igraph, knitr, phangorn, prettydoc, testthat, tidyr, vroom, xml2 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | ggtree |
Suggests Me | MicrobiotaProcess, rfaRm |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | treeio_1.12.0.tar.gz |
Windows Binary | treeio_1.12.0.zip |
macOS 10.13 (High Sierra) | treeio_1.12.0.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 3.11 | Source Archive |