The UCSCXenaTools R package

The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq - Published in JOSS (2019)

https://github.com/ropensci/ucscxenatools

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:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/

README.Rmd

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output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# UCSCXenaTools 



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**UCSCXenaTools** is an R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. 
Public omics data from UCSC Xena are supported through [**multiple turn-key Xena Hubs**](https://xenabrowser.net/datapages/), which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.

**Who is the target audience and what are scientific applications of this package?**

* Target Audience: cancer and clinical researchers, bioinformaticians
* Applications: genomic and clinical analyses

## Table of Contents

* [Installation](#installation)
* [Data Hub List](#data-hub-list)
* [Basic usage](#basic-usage)
* [Citation](#citation)
* [How to contribute](#how-to-contribute)
* [Acknowledgment](#acknowledgment)

## Installation

Install stable release from r-universe/CRAN with:

```{r, eval=FALSE}
install.packages('UCSCXenaTools', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))
#install.packages("UCSCXenaTools")
```

You can also install devel version of **UCSCXenaTools** from github with:

```{r gh-installation, eval = FALSE}
# install.packages("remotes")
remotes::install_github("ropensci/UCSCXenaTools")
```

If you want to build vignette in local, please add two options:

```{r, eval=FALSE}
remotes::install_github("ropensci/UCSCXenaTools", build_vignettes = TRUE, dependencies = TRUE)
```

## Data Hub List

All datasets are available at .

Currently, **UCSCXenaTools** supports the following data hubs of UCSC Xena.

* UCSC Public Hub: 
* TCGA Hub: 
* GDC Xena Hub (new): 
* GDC v18.0 Xena Hub (old): 
* ICGC Xena Hub: 
* Pan-Cancer Atlas Hub: 
* UCSC Toil RNAseq Recompute Compendium Hub: 
* PCAWG Xena Hub: 
* ATAC-seq Hub: 
* Treehouse Xena Hub: 
* ...

Users can update dataset list from the newest version of UCSC Xena by hand with `XenaDataUpdate()` function, followed
by restarting R and `library(UCSCXenaTools)`.

If any url of data hub is changed or a new data hub is online, please remind me by emailing to  or [opening an issue on GitHub](https://github.com/ropensci/UCSCXenaTools/issues).


## Basic usage

Download UCSC Xena datasets and load them into R by **UCSCXenaTools** is a workflow with `generate`, `filter`, `query`, `download` and `prepare` 5 steps, which are implemented as `XenaGenerate`, `XenaFilter`, `XenaQuery`, `XenaDownload` and `XenaPrepare` functions, respectively. They are very clear and easy to use and combine with other packages like `dplyr`.

To show the basic usage of **UCSCXenaTools**, we will download clinical data of LUNG, LUAD, LUSC from TCGA (hg19 version) data hub. Users can learn more about **UCSCXenaTools** by running `browseVignettes("UCSCXenaTools")` to read vignette.

### XenaData data.frame

**UCSCXenaTools** uses a `data.frame` object (built in package) `XenaData` to generate an instance of `XenaHub` class, which records information of all datasets of UCSC Xena Data Hubs.

You can load `XenaData` after loading `UCSCXenaTools` into R.

```{r}
library(UCSCXenaTools)
data(XenaData)

head(XenaData)
```

### Workflow

Select datasets.

```{r}
# The options in XenaFilter function support Regular Expression
XenaGenerate(subset = XenaHostNames=="tcgaHub") %>% 
  XenaFilter(filterDatasets = "clinical") %>% 
  XenaFilter(filterDatasets = "LUAD|LUSC|LUNG") -> df_todo

df_todo
```

Query and download.

```{r}
XenaQuery(df_todo) %>%
  XenaDownload() -> xe_download
```

Prepare data into R for analysis.

```{r}
cli = XenaPrepare(xe_download)
class(cli)
names(cli)
```

## More to read

- [Introduction and basic usage of UCSCXenaTools](https://shixiangwang.github.io/home/en/tools/ucscxenatools-intro/)
- [UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis](https://shixiangwang.github.io/home/en/post/ucscxenatools-201908/)
- [Obtain RNAseq Values for a Specific Gene in Xena Database](https://shixiangwang.github.io/home/en/post/2020-07-22-ucscxenatools-single-gene/)
- [UCSC Xena Access APIs in UCSCXenaTools](https://shixiangwang.github.io/home/en/tools/ucscxenatools-api/)

## Citation

Cite me by the following paper.

```
Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
  from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. 
  Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627

# For BibTex
  
@article{Wang2019UCSCXenaTools,
	journal = {Journal of Open Source Software},
	doi = {10.21105/joss.01627},
	issn = {2475-9066},
	number = {40},
	publisher = {The Open Journal},
	title = {The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq},
	url = {https://dx.doi.org/10.21105/joss.01627},
	volume = {4},
	author = {Wang, Shixiang and Liu, Xuesong},
	pages = {1627},
	date = {2019-08-05},
	year = {2019},
	month = {8},
	day = {5},
}
```

Cite UCSC Xena by the following paper. 

```
Goldman, Mary, et al. "The UCSC Xena Platform for cancer genomics data 
    visualization and interpretation." BioRxiv (2019): 326470.
```

## How to contribute

For anyone who wants to contribute, please follow the guideline:

* Clone project from GitHub
* Open `UCSCXenaTools.Rproj` with RStudio
* Modify source code 
* Run `devtools::check()`, and fix all errors, warnings and notes
* Create a pull request

## Acknowledgment

This package is based on [XenaR](https://github.com/mtmorgan/XenaR), thanks [Martin Morgan](https://github.com/mtmorgan) for his work.

[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)

Owner

JOSS Publication

The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq

Published

August 05, 2019

DOI

10.21105/joss.01627

Volume 4, Issue 40, Page 1627

Authors

Shixiang Wang
School of Life Science and Technology, ShanghaiTech University, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences

Xuesong Liu
School of Life Science and Technology, ShanghaiTech University

Editor

Arfon Smith

Tags

cancer genomics data access

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