treeio
Base Classes and Functions for Phylogenetic Tree Input and Output
Bioconductor version: 3.23 · Package version: 1.36.1
'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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("treeio") Details
| Maintainer | Guangchuang Yu <guangchuangyu@gmail.com> |
| Author | Guangchuang Yu [aut, cre] (ORCID: <https://orcid.org/0000-0002-6485-8781>), Tommy Tsan-Yuk Lam [ctb, ths], Shuangbin Xu [ctb] (ORCID: <https://orcid.org/0000-0003-3513-5362>), Bradley Jones [ctb], Casey Dunn [ctb], Tyler Bradley [ctb], Konstantinos Geles [ctb] |
| License | Artistic-2.0 |
| URL | https://yulab-smu.top/contribution-tree-data/ |
| Bug Reports | https://github.com/YuLab-SMU/treeio/issues |
| Downloads rank | 29900 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software |
Documentation
Download
Dependencies
Depends: R (>= 4.1.0)
Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)
Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
Reverse dependencies
Imports Me (11): BioVizSeq, dowser, EvoPhylo, geneplast.data, ggtree, lefser, MicrobiotaProcess, RevGadgets, RPesto, shinyTempSignal, TreeSummarizedExperiment
Suggests Me (8): FossilSim, ggtreeDendro, ggtreeExtra, idiogramFISH, MetaNet, nosoi, rfaRm, treestructure