Datasets
Models
Downloads: 1
Switch to side-by-side view
--- a/README.md +++ b/README.md @@ -1,253 +1,195 @@ - -<!-- README.md is generated from README.Rmd. Please edit that file --> - -# 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 -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 -# 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 <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) -#> ========================================================================================= -#> 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. - -``` 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 -#> 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. - -``` 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. - -[](https://ropensci.org) +--- +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-" +) +``` + + +<!-- 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)