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Bioconductor - ggtree (development version)

ggtree

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

an R package for visualization of tree and annotation data

Bioconductor version: Development (3.22)

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

Author: Guangchuang Yu [aut, cre, cph] ORCID: 0000-0002-6485-8781 , Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] ORCID: 0000-0003-3513-5362 , Lin Li [ctb], Bradley Jones [ctb], Justin Silverman [ctb], Watal M. Iwasaki [ctb], Yonghe Xia [ctb], Ruizhu Huang [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Citation (from within R, enter citation("ggtree")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

BiocManager::install("ggtree")

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("ggtree")
Details biocViews Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization Version 3.17.0 In Bioconductor since BioC 3.1 (R-3.2) (10 years) License Artistic-2.0 Depends R (>= 3.5.0) Imports ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio(>= 1.8.0), utils, scales, stats, cli System Requirements URL https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/(book) http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628(paper) Bug Reports https://github.com/YuLab-SMU/ggtree/issues See More Suggests emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue Linking To Enhances Depends On Me ggtreeDendro, tanggle Imports Me cardelino, cogeqc, crumblr, enrichplot, ggmsa, ggtreeExtra, ggtreeSpace, gINTomics, iSEEtree, lefser, LinTInd, LymphoSeq, miaViz, MicrobiotaProcess, mitology, orthogene, philr, scBubbletree, scDotPlot, sitePath, SVP, systemPipeTools, treeclimbR, treekoR, BioVizSeq, DAISIEprep, ddtlcm, delimtools, dowser, EvoPhylo, FossilSim, genBaRcode, harrietr, numbat, Platypus, RevGadgets, scistreer, shinyTempSignal, STraTUS, Sysrecon, TransProR Suggests Me compcodeR, syntenet, TreeAndLeaf, treeio, TreeSummarizedExperiment, universalmotif, aplot, aplotExtra, CoOL, DAISIE, deeptime, gggenomes, ggimage, ggtangle, idiogramFISH, MetaNet, nosoi, oppr, PCMBase, pctax, RAINBOWR, rhierbaps, rphylopic Links To Me Build Report Build Report Package Archives

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


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