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--- a +++ b/README.Rmd @@ -0,0 +1,196 @@ +--- +output: github_document +--- + +<!-- README.md is generated from README.Rmd. Please edit that file --> + +```{r, echo = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + fig.path = "README-" +) +``` + +# UCSCXenaTools <img src='man/figures/logo.png' align="right" height="200" alt="logo"/> + +<!-- badges: start --> + +[](https://cran.r-project.org/package=UCSCXenaTools) +[](https://lifecycle.r-lib.org/articles/stages.html) +[](https://github.com/ropensci/UCSCXenaTools/actions/workflows/main.yml) +[](https://cran.r-project.org/package=UCSCXenaTools) +[](https://github.com/ropensci/software-review/issues/315) +[](https://doi.org/10.21105/joss.01627) + +<!-- badges: end --> + +**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. + +[](https://ropensci.org)