Authors: Raymond Tong, Yuki Chan
Working with Shiny for 1+ years
Abstract: GenePiper is a standalone R shiny application for NGS data mining. It provides over 20 different analysis methods with user-friendly GUI. Recently, 6 main categories of analytic modules (Diversity, Descriptive, Oridination, Correlation, Clustering and Non-parametric test) are included
Full Description: Can I do this easily?
The principle of GenePiper is simple - Make our life easier.
NGS data mining involves many packages, many tools, many commands and many different data format. We need to switch between different data format, transform data tables with different tools to fit the data into different analytical test packages. The routine data transformation work usually take up more than half of the data analysis time.
GenePiper is designed to take care of all these routine and tedious tasks. The data is imported once and saved. GenePiper will handle all the process from converting the raw data to getting the result from different analysis. User can easily subset their data and save for future use or subset data ad hoc for each analysis.
The GUI of GenePiper is based on R Shiny package which seamlessly connects the interactive interface to the data analysis process. GenePiper provides different parameters for user to fine tune the analysis and test different grouping setting.
xxxx:error exit status 1?
NGS data mining involves many packages and tools. The installation of all these packages sometimes causes more trouble than using them. New package may conflict with the existing one. Installation may fail because of missing library. Package version may not be compatible.
To address the above problem, GenePiper is built in a clean virtual environment via VirtualBox. The isolated environment provides consistency during installation. Through Vagrant, the installation of GenePiper becomes easier using only one command.
Did our data safe?
Most NGS data being analysed are unpublished data. The security of data are also the main concern when using cloud apps provided by others. So, GenePiper installed in the virtual environment on user's own computer can address this problem and ensure the data security.
For detailed walkthrough of GenePiper, please refer the following link
Keywords: NGS, data mining, 16S, integrated environment , gui
Shiny app: Nil
RStudio Cloud: Nil