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# UCSCXenaTools <img src='man/figures/logo.png' align="right" height="200" alt="logo"/>

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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 <https://xenabrowser.net/datapages/>.

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

* UCSC Public Hub: <https://ucscpublic.xenahubs.net/>

* TCGA Hub: <https://tcga.xenahubs.net/>

* GDC Xena Hub (new): <https://gdc.xenahubs.net/>

* GDC v18.0 Xena Hub (old): <https://gdcV18.xenahubs.net/>

* ICGC Xena Hub: <https://icgc.xenahubs.net/>

* Pan-Cancer Atlas Hub: <https://pancanatlas.xenahubs.net/>

* UCSC Toil RNAseq Recompute Compendium Hub: <https://toil.xenahubs.net/>

* PCAWG Xena Hub: <https://pcawg.xenahubs.net/>

* ATAC-seq Hub: <https://atacseq.xenahubs.net/>

* Singel Cell Xena Hub: <https://singlecellnew.xenahubs.net/> (**Disabled by UCSCXena**)

* Kids First Xena Hub: <https://kidsfirst.xenahubs.net/>

* Treehouse Xena Hub: <https://xena.treehouse.gi.ucsc.edu:443/>

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 <w_shixiang@163.com> 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.

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