UCSCXenaTools

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, 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
• Data Hub List
• Basic usage
• Citation
• How to contribute
• Acknowledgment

Installation

Install stable release from r-universe/CRAN with:

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:

# install.packages("remotes")
remotes::install_github("ropensci/UCSCXenaTools")

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

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 [email protected] or opening an issue on GitHub.

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.

library(UCSCXenaTools)
#> =========================================================================================
#> UCSCXenaTools version 1.6.0
#> Project URL: https://github.com/ropensci/UCSCXenaTools
#> Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
#> 
#> If you use it in published research, please cite:
#> 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
#> =========================================================================================
#>                               --Enjoy it--
data(XenaData)

head(XenaData)
#> # A tibble: 6 × 17
#>   XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
#>   <chr>     <chr>         <chr>       <chr>              <int> <chr>       <chr>
#> 1 https://… publicHub     Breast Can… ucsfNeve_pu…          51 gene expre… Neve…
#> 2 https://… publicHub     Breast Can… ucsfNeve_pu…          57 phenotype   Phen…
#> 3 https://… publicHub     Glioma (Ko… kotliarov20…         194 copy number Kotl…
#> 4 https://… publicHub     Glioma (Ko… kotliarov20…         194 phenotype   Phen…
#> 5 https://… publicHub     Lung Cance… weir2007_pu…         383 copy number CGH  
#> 6 https://… publicHub     Lung Cance… weir2007_pu…         383 phenotype   Phen…
#> # ℹ 10 more variables: Type <chr>, AnatomicalOrigin <chr>, SampleType <chr>,
#> #   Tags <chr>, ProbeMap <chr>, LongTitle <chr>, Citation <chr>, Version <chr>,
#> #   Unit <chr>, Platform <chr>

Workflow

Select datasets.

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

df_todo
#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (3 total):
#>   TCGA Lung Cancer (LUNG)
#>   TCGA Lung Adenocarcinoma (LUAD)
#>   TCGA Lung Squamous Cell Carcinoma (LUSC)
#> datasets() (3 total):
#>   TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
#>   TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#>   TCGA.LUSC.sampleMap/LUSC_clinicalMatrix

Query and download.

XenaQuery(df_todo) %>%
  XenaDownload() -> xe_download
#> This will check url status, please be patient.
#> All downloaded files will under directory /tmp/RtmpYsoGw3.
#> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
#> Creating directories for datasets...
#> Downloading TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
#> Downloading TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#> Downloading TCGA.LUSC.sampleMap/LUSC_clinicalMatrix

Prepare data into R for analysis.

cli = XenaPrepare(xe_download)
class(cli)
#> [1] "list"
names(cli)
#> [1] "LUNG_clinicalMatrix" "LUAD_clinicalMatrix" "LUSC_clinicalMatrix"

More to read

• Introduction and basic usage of UCSCXenaTools
• UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis
• Obtain RNAseq Values for a Specific Gene in Xena Database
• UCSC Xena Access APIs in UCSCXenaTools

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, thanks Martin Morgan for his work.