Download and Explore Datasets from UCSC Xena Data Hubs

Download and explore datasets from UCSC Xena data 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.

UCSCXenaTools is an R package for downloading and exploring data from UCSC Xena data 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.

Table of Contents

• Installation
• Data Hub List
• Usage
• Documentation
• Citation
• Acknowledgement
• LICENSE
• Code of conduct

Installation

Install stable release from CRAN with:

install.packages("UCSCXenaTools")

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

# install.packages("remotes")
remotes::install_github("ShixiangWang/UCSCXenaTools", build_vignettes = TRUE)

Data Hub List

All datasets are available at https://xenabrowser.net/datapages/.

Currently, UCSCXenaTools supports all 9 data hubs of UCSC Xena.

• UCSC Public Hub: https://ucscpublic.xenahubs.net
• TCGA Hub: https://tcga.xenahubs.net
• GDC Xena Hub: https://gdc.xenahubs.net
• ICGC Xena Hub: https://icgc.xenahubs.net
• Pan-Cancer Atlas Hub: https://pancanatlas.xenahubs.net
• GA4GH (TOIL) Hub: https://toil.xenahubs.net
• Treehouse Hub: https://xena.treehouse.gi.ucsc.edu
• PCAWG: https://pcawg.xenahubs.net
• ATAC-seq: https://atacseq.xenahubs.net

If the url of data hub changed, please remind me by emailing to [email protected] or opening an issue on GitHub.

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 download clinical data of LUNG, LUAD, LUSC from TCGA (hg19 version) data hub.

XenaData data.frame

UCSCXenaTools uses a data.frame object (built in package) XenaData to generate an instance of XenaHub class, which communicates with API of UCSC Xena Data Hubs.

You can load XenaData after loading UCSCXenaTools into R.

library(UCSCXenaTools)
#> =========================================================================
#> UCSCXenaTools version 1.0.0
#> Github page: https://github.com/ShixiangWang/UCSCXenaTools
#> Documentation: https://github.com/ShixiangWang/UCSCXenaTools
#> If you use it in published research, please cite:
#> Wang, Shixiang, et al. "APOBEC3B and APOBEC mutational signature
#>     as potential predictive markers for immunotherapy
#>     response in non-small cell lung cancer." Oncogene (2018).
#> =========================================================================
#> 
data(XenaData)
 
head(XenaData)
#>                         XenaHosts XenaHostNames
#> 1 https://ucscpublic.xenahubs.net   UCSC_Public
#> 2 https://ucscpublic.xenahubs.net   UCSC_Public
#> 3 https://ucscpublic.xenahubs.net   UCSC_Public
#> 4 https://ucscpublic.xenahubs.net   UCSC_Public
#> 5 https://ucscpublic.xenahubs.net   UCSC_Public
#> 6 https://ucscpublic.xenahubs.net   UCSC_Public
#>                                     XenaCohorts
#> 1 Acute lymphoblastic leukemia (Mullighan 2008)
#> 2 Acute lymphoblastic leukemia (Mullighan 2008)
#> 3 Acute lymphoblastic leukemia (Mullighan 2008)
#> 4                   Breast Cancer (Caldas 2007)
#> 5                   Breast Cancer (Caldas 2007)
#> 6                   Breast Cancer (Caldas 2007)
#>                                               XenaDatasets
#> 1    mullighan2008_public/mullighan2008_500K_genomicMatrix
#> 2 mullighan2008_public/mullighan2008_public_clinicalMatrix
#> 3    mullighan2008_public/mullighan2008_SNP6_genomicMatrix
#> 4              Caldas2007/chinSF2007_public_clinicalMatrix
#> 5             Caldas2007/chinSFGenomeBio2007_genomicMatrix
#> 6                   Caldas2007/naderi2007Exp_genomicMatrix

Workflow

Select datasets.

# The options in XenaFilter function support Regular Expression
XenaGenerate(subset = XenaHostNames=="TCGA") %>% 
  XenaFilter(filterDatasets = "clinical") %>% 
  XenaFilter(filterDatasets = "LUAD|LUSC|LUNG") -> df_todo
 
df_todo
#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (3 total):
#>   TCGA Lung Adenocarcinoma (LUAD)
#>   TCGA Lung Cancer (LUNG)
#>   TCGA Lung Squamous Cell Carcinoma (LUSC)
#> datasets() (3 total):
#>   TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#>   TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
#>   TCGA.LUSC.sampleMap/LUSC_clinicalMatrix

Query and download.

XenaQuery(df_todo) %>%
  XenaDownload() -> xe_download
#> This will check url status, please be patient.
#> We will download files to directory /var/folders/mx/rfkl27z90c96wbmn3_kjk8c80000gn/T//RtmpOTE23c.
#> Downloading TCGA.LUAD.sampleMap__LUAD_clinicalMatrix.gz
#> Downloading TCGA.LUNG.sampleMap__LUNG_clinicalMatrix.gz
#> Downloading TCGA.LUSC.sampleMap__LUSC_clinicalMatrix.gz
#> Note file names inherit from names in datasets column
#>   and '/' all changed to '__'.

Prepare data into R for analysis.

cli = XenaPrepare(xe_download)
class(cli)
#> [1] "list"
names(cli)
#> [1] "TCGA.LUAD.sampleMap__LUAD_clinicalMatrix.gz"
#> [2] "TCGA.LUNG.sampleMap__LUNG_clinicalMatrix.gz"
#> [3] "TCGA.LUSC.sampleMap__LUSC_clinicalMatrix.gz"

Browse datasets

Create two XenaHub objects:

• to_browse - a XenaHub object contains a cohort and a dataset.
• to_browse2 - a XenaHub object contains 2 cohorts and 2 datasets.

XenaGenerate(subset = XenaHostNames=="TCGA") %>%
    XenaFilter(filterDatasets = "clinical") %>%
    XenaFilter(filterDatasets = "LUAD") -> to_browse
 
to_browse
#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (1 total):
#>   TCGA Lung Adenocarcinoma (LUAD)
#> datasets() (1 total):
#>   TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
 
XenaGenerate(subset = XenaHostNames=="TCGA") %>%
    XenaFilter(filterDatasets = "clinical") %>%
    XenaFilter(filterDatasets = "LUAD|LUSC") -> to_browse2
 
to_browse2
#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (2 total):
#>   TCGA Lung Adenocarcinoma (LUAD)
#>   TCGA Lung Squamous Cell Carcinoma (LUSC)
#> datasets() (2 total):
#>   TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#>   TCGA.LUSC.sampleMap/LUSC_clinicalMatrix

XenaBrowse() function can be used to browse dataset/cohort links using your default web browser. At default, this function limit one dataset/cohort for preventing user to open too many links at once.

# This will open you web browser
XenaBrowse(to_browse)
 
XenaBrowse(to_browse, type = "cohort")

# This will throw error
XenaBrowse(to_browse2)
#> Error in XenaBrowse(to_browse2): This function limite 1 dataset to browse.
#>  Set multiple to TRUE if you want to browse multiple links.
 
XenaBrowse(to_browse2, type = "cohort")
#> Error in XenaBrowse(to_browse2, type = "cohort"): This function limite 1 cohort to browse. 
#>  Set multiple to TRUE if you want to browse multiple links.

When you make sure you want to open multiple links, you can set multiple option to TRUE.

XenaBrowse(to_browse2, multiple = TRUE)
XenaBrowse(to_browse2, type = "cohort", multiple = TRUE)

Documentation

More features and usages please read online documentation on CRAN or Github website.

Citation

Wang, Shixiang, et al. “APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer.” Oncogene (2018).

Acknowledgement

This package is based on XenaR, thanks Martin Morgan for his work.

LICENSE

GPL-3

please note, code from XenaR package under Apache 2.0 license.

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.