Omics Playground是一個免費(fèi)的生信分析平臺，可以用于組學(xué)數(shù)據(jù)的可視化、分析和挖掘。適用于沒有任何計算基礎(chǔ)的生物小白，界面友好、圖形可視化，沒有任何編程經(jīng)驗的人都能用。
參考文獻(xiàn)：Murodzhon Akhmedov, Axel Martinelli, Roger Geiger, Ivo Kwee. Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data. NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqz019
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（1）此工具所能做的事情的示意圖，還是很不錯的，很多生信常規(guī)的工具都包含進(jìn)來了。
（2）除了在線版本，工具還有本地版，有兩種安裝方式。需要的同學(xué)自取。
（2.1) Run using the Docker file
The docker file of the platform is available on Docker Hub. Follow the steps below to set up a running platform from the docker file:
- Pull the docker image using the command:
docker pull bigomics/omicsplayground
- Then run the docker with:
docker run --rm -p 4000:3838 bigomics/omicsplayground
Open
http://localhost:4000in your browser to run the platform.If you want to include your own pgx files into the platform Datasets tab, select the local folder in which you have stored your pgx files under “Host Path” in the optional settings in docker. Also type “/omicsplayground/data” in the “Container Path” box.
(2.2)Run from source code
Omics Playground is implemented in R using the Shiny Server web application framework. You will need R and Shiny Server installed to run Omics Playground.
The source code of the platform is available on GitHub. You can download the latest release of the software by cloning the repository. Below, we explain the steps required to set up the platform from the source code:
- Clone the GitHub repository using:
git clone https://github.com/bigomics/omicsplayground.git
- Install all necessary R packages by running the script in the
R/folder:
Rscript requirements.R
- Run the following command in the
build/folder to build the datasets:
Rscript build-datasets.R
Note:
Building the datasets can vary from minutes to a couple of hours depending on their sizes.
- Change the current directory into the
shiny/folder and execute the following command to run the platform:
R -e "rmarkdown::run(shiny_args=list(launch.browser=TRUE))"
If you have Shiny Server installed you can create a link to the shiny folder in the system-wide shiny-server apps folder or in your ShinyApps user folder.
