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 (3.24)
'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("treeio")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| treeio | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software |
| Version | 1.37.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| Imports | ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6) |
| System Requirements | |
| URL | https://yulab-smu.top/contribution-tree-data/ |
| Bug Reports | https://github.com/YuLab-SMU/treeio/issues |
See More
| Suggests | Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | ggtree, lefser, MicrobiotaProcess, TreeSummarizedExperiment, geneplast.data, BioVizSeq, dowser, EvoPhylo, RevGadgets, RPesto, shinyTempSignal |
| Suggests Me | ggtreeDendro, ggtreeExtra, rfaRm, FossilSim, idiogramFISH, MetaNet, nosoi, treestructure |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | treeio_1.37.0.tar.gz |
| Windows Binary (x86_64) | treeio_1.37.0.zip |
| macOS Binary (big-sur-x86_64) | treeio_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | treeio_1.37.0.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 |