treeio

:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output

https://github.com/yulab-smu/treeio

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 5 DOI reference(s) in README
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Academic publication links
Links to: wiley.com
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Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary

Keywords

exporter parser phylogenetic-trees

Last synced: 4 months ago · JSON representation

Repository

:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output

Basic Info

Host: GitHub
Owner: YuLab-SMU
Language: R
Default Branch: devel
Homepage: https://yulab-smu.top/treedata-book/
Size: 3 MB

Statistics

Stars: 102
Watchers: 13
Forks: 26
Open Issues: 29
Releases: 0

Topics

exporter parser phylogenetic-trees

Created about 9 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing Codemeta

README.Rmd

---
output:
  md_document:
    variant: gfm
html_preview: false
---




#  treeio: Base classes and functions for phylogenetic tree input and output 

```{r echo=FALSE, results="hide", message=FALSE}
#library("txtplot")
library("badger")
library("ypages")

library("yulab.utils")
```

[![](https://badges.ropensci.org/179_status.svg)](https://github.com/ropensci/onboarding/issues/179)
[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/treeio.svg)](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#since)
[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![platform](http://www.bioconductor.org/shields/availability/devel/treeio.svg)](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#archives)
[![codecov](https://codecov.io/gh/GuangchuangYu/treeio/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/treeio)


`r badge_bioc_release("treeio", "green")`
`r badge_devel("guangchuangyu/treeio", "green")`
[![Linux Travis Build Status](https://img.shields.io/travis/GuangchuangYu/treeio/master.svg?label=Linux)](https://travis-ci.org/GuangchuangYu/treeio)
[![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/treeio/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/treeio)


`r badge_bioc_download("treeio", "total", "blue")`
`r badge_bioc_download("treeio", "month", "blue")`
`r badge_bioc_download_rank("treeio")`



```{r comment="", echo=FALSE, results='asis'}
cat(packageDescription('treeio')$Description)
```

Visit  for details.


[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=treeio&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
`r badger::badge_custom("follow me on", "WeChat", "green", "https://yulab-smu.top/images/biobabble.jpg")`




## :writing_hand: Authors

Guangchuang YU 

School of Basic Medical Sciences, Southern Medical University



If you use `r Biocpkg('treeio')` in published research, please cite:

+ LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, __G Yu__^\*^. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. __*Molecular Biology and Evolution*__. 2020, 37(2):599-603. doi: [10.1093/molbev/msz240](http://dx.doi.org/10.1093/molbev/msz240).


## :arrow_double_down: Installation

Get the released version from Bioconductor:

```r
## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("treeio")
```

Or the development version from github:

```r
## install.packages("devtools")
devtools::install_github("YuLab-SMU/treeio")
```



## :sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to
abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).


## :houses: Package Affiliations

The `treeio` package is a part of the Bioconductor and rOpenSci projects.

| [![bioconductor_footer](http://bioconductor.org/images/logo_bioconductor.gif)](http://bioconductor.org) | [![ropensci_footer](http://ropensci.org/public_images/github_footer.png)](http://ropensci.org) |
|:-------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------:|

Owner

Name: Bioinformatics Group @ SMU
Login: YuLab-SMU
Kind: organization
Email: gcyu1@smu.edu.cn
Location: Guangzhou

Website: https://yulab-smu.top
Repositories: 76
Profile: https://github.com/YuLab-SMU

Research group led by Prof. Guangchuang Yu in School of Basic Medical Sciences, Southern Medical University

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Dependencies

DESCRIPTION cran

R >= 3.6.0 depends
ape * imports
dplyr * imports
jsonlite * imports
magrittr * imports
methods * imports
rlang * imports
tibble * imports
tidytree >= 0.3.9 imports
utils * imports
Biostrings * suggests
ggplot2 * suggests
ggtree * suggests
igraph * suggests
knitr * suggests
phangorn * suggests
prettydoc * suggests
rmarkdown * suggests
testthat * suggests
tidyr * suggests
vroom * suggests
xml2 * suggests
yaml * suggests

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