knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
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?
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("ropensci/UCSCXenaTools")
If you want to build vignette in local, please add two options:
remotes::install_github("ropensci/UCSCXenaTools", build_vignettes = TRUE, dependencies = TRUE)
The minimum versions to run the vignette is 1.2.4
.
GitHub Issue is a place for discussing any problem.
All datasets are available at https://xenabrowser.net/datapages/.
Currently, UCSCXenaTools supports the following data hubs of UCSC Xena.
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.
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.
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) data(XenaData) head(XenaData)
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
Sometimes we only know some keywords, XenaScan()
can be used to scan all rows to detect if
the keywords exist in XenaData
.
x1 = XenaScan(pattern = 'Blood') x2 = XenaScan(pattern = 'LUNG', ignore.case = FALSE) x1 %>% XenaGenerate() x2 %>% XenaGenerate()
Query and download.
XenaQuery(df_todo) %>% XenaDownload() -> xe_download
For researchers in China, now Hiplot team 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.
options(use_hiplot = TRUE) XenaQuery(df_todo) %>% XenaDownload() -> xe_download
Prepare data into R for analysis.
cli = XenaPrepare(xe_download) class(cli) names(cli)
Create two XenaHub objects:
to_browse
- a XenaHub object containing a cohort and a dataset.to_browse2
- a XenaHub object containing 2 cohorts and 2 datasets.XenaGenerate(subset = XenaHostNames=="tcgaHub") %>% XenaFilter(filterDatasets = "clinical") %>% XenaFilter(filterDatasets = "LUAD") -> to_browse to_browse XenaGenerate(subset = XenaHostNames=="tcgaHub") %>% XenaFilter(filterDatasets = "clinical") %>% XenaFilter(filterDatasets = "LUAD|LUSC") -> to_browse2 to_browse2
XenaBrowse()
function can be used to browse dataset/cohort links using your default web browser.
At default, this function limits 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) XenaBrowse(to_browse2, type = "cohort")
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)
The core functionality has been described above. I write more usages about this package in my website but not here because sometimes package check will fail due to internet problem.
Read Obtain RNAseq Values for a Specific Gene in Xena Database to see how to get values for single gene. A use case for survival analysis based on single gene expression has been published on rOpenSci, please read UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis.
Thanks to the UCSC Xena team, the new feature 'resume from breakpoint' is added and
can be done by XenaDownload() with the method
and extra
flags specified.
Of note, the corresponding wget
or curl
command must be installed by your OS
and can be found by R.
The folliwng code gives a test example, the data can be viewed on web page.
library(UCSCXenaTools) xe = XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_expected_count") xe xq = XenaQuery(xe) # You cannot resume from breakpoint in default mode XenaDownload(xq, destdir = "~/test/", force = TRUE) # You can do it with 'curl' command XenaDownload(xq, destdir = "~/test/", method = "curl", extra = "-C -", force = TRUE) # You can do it with 'wget' command XenaDownload(xq, destdir = "~/test/", method = "wget", extra = "-c", force = TRUE)
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 = {http://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.
This package is based on XenaR, thanks Martin Morgan for his work.
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