Usage	Release	Development

# 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**](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 CRAN with: ``` r install.packages("UCSCXenaTools") ``` You can also install devel version of **UCSCXenaTools** from github with: ``` r # install.packages("remotes") remotes::install_github("ropensci/UCSCXenaTools") ``` If you want to build vignette in local, please add two options: ``` r 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: - ICGC Xena Hub: - Pan-Cancer Atlas Hub: - UCSC Toil RNAseq Recompute Compendium Hub: - PCAWG Xena Hub: - ATAC-seq Hub: - Singel Cell Xena Hub: - Kids First Xena 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) #> ========================================================================================= #> UCSCXenaTools version 1.4.0 #> 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 x 17 #> XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label #> #> 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… #> # … with 10 more variables: Type , AnatomicalOrigin , #> # SampleType , Tags , ProbeMap , LongTitle , #> # Citation , Version , Unit , Platform ``` ### 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 #> 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. ``` r XenaQuery(df_todo) %>% XenaDownload() -> xe_download ``` **For researchers in China, now [Hiplot team](https://hiplot.com.cn/) has deployed several Xena [mirror sites](https://xena.hiplot.com.cn/) at Shanghai. You can set an option `options(use_hiplot = TRUE)` before querying data step to speed up both data querying and downloading.** ``` r options(use_hiplot = TRUE) XenaQuery(df_todo) %>% XenaDownload() -> xe_download #> Use hiplot server (China) for mirrored data hubs (set 'options(use_hiplot = FALSE)' to disable it) #> This will check url status, please be patient. #> All downloaded files will under directory /var/folders/mx/rfkl27z90c96wbmn3_kjk8c80000gn/T//RtmpbjgG9I. #> 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. ``` r 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](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)

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