2021-08-05 Omics Playground在线转录组

网站链接

Omics Playground是一个免费的生信分析平台，可以用于组学数据的可视化、分析和挖掘。适用于没有任何计算基础的生物小白，界面友好、图形可视化，没有任何编程经验的人都能用。
参考文献：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图，还是很不错的，很多生信常规的工具都包含进来了。

overview.png

（2）除了在线版本，工具还有本地版，有两种安装方式。需要的同学自取。

（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:

1. Pull the docker image using the command:

docker pull bigomics/omicsplayground

2. Then run the docker with:

docker run --rm -p 4000:3838 bigomics/omicsplayground

3. Open http://localhost:4000 in your browser to run the platform.

4. 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:

1. Clone the GitHub repository using:

git clone https://github.com/bigomics/omicsplayground.git

2. Install all necessary R packages by running the script in the R/ folder:

Rscript requirements.R

3. 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.

4. 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.