UCSCXenaShiny

CRAN status lifecycle R-CMD-check Lines Of Code

UCSCXenaShiny is an R package for interactively exploring UCSC Xena. It is mainly designed to provide a web app (built on the top of {shiny} framework and {UCSCXenaTools} package) for downloading, analyzing and visualizing datasets from UCSC Xena.

Please cite the following article when you used UCSCXenaShiny in your study:


Wang, S.; Xiong, Y.; Gu, K.; Zhao, L.; Li, Y.; Zhao, F.; Li, X.; Liu, X. UCSCXenaShiny: An R Package for Exploring and Analyzing UCSC Xena Public Datasets in Web Browser. Preprints 2020, 2020070179 (doi: 10.20944/preprints202007.0179.v1).


:cloud: Use on cloud

If you don’t want to install R and packages locally, or you have no programming experience, try using this tool on Hiplot platform: https://shiny.hiplot.com.cn/ucsc-xena-shiny/.

:arrow_double_down: Installation

You can install stable release of UCSCXenaShiny from CRAN with:

install.packages("UCSCXenaShiny")

You can install the development version of UCSCXenaShiny from Github with:

remotes::install_github("openbiox/XenaShiny")

Or Gitee (for Chinese users):

remotes::install_git("https://gitee.com/XenaShiny/UCSCXenaShiny")

:beginner: Usage

First load package:

library(UCSCXenaShiny)

Start Shiny in your R console (ignore this if you just want to use functions in this package):

app_run()
# At default, the Shiny is running under client mode
# It means the data queried from remote UCSC Xena server will
# be saved to temporary directory determined by R
# If you frequently use this tool or deploy this tool as a web service for multiple users
# It is recommended to run it with 'server' mode
# i.e.,
#
# app_run("server")

If you want deploy UCSC Xena Shiny with Shiny Server, please copy App.R and www/ directory under shinyapp. xena.runMode on the top of App.R is recommended to set as "server" instead of "client" (default).

For advanced users, examples for illustrating useful functions to obtain and analyze data are described in vignette.

All exported data and functions are organized at here.

xena.cacheDir and xena.zenodoDir are two options to control where to store data.

e.g.,

options(xena.cacheDir = "/home/xxx/xena_data")

Option xena.runMode can be used to control the way how the Shiny works. It can be ‘client’ or ‘server’. You can directly set it in app_run().

:hammer_and_wrench: Troubleshooting

It seems that your operating system lacks gmp and Rmpfr development libraries.

If you use Ubuntu, you can install these dependencies:

sudo apt-get install libgmp3-dev
sudo apt-get install libmpfr-dev

:writing_hand: Author

:page_with_curl: LICENSE

MIT © Openbiox