This wiki page contains the following contents:
GMM is the official name of the web implementation kickstarted by the 2024 semester 1 intake. The codebase can be found here.
The specifications for the web application can be found in the Problem Space wiki page.
This implementation was written in R Shiny to set up the web environment, and Python which handles the FACS merge logic. For more information on the technologies used, visit the Dependencies section.
- Easy to use interface which only requires a folder upload, a processing and download buttons
- Readily to use on WEHI's Milton HPC Ondemand's R Shiny servers
- Output preview upon clicking process button
- Ability to download output into multiple formats including CSV, TSV and excel
- Popup image guides for what the input files should look like
Please use unix/linux based environment for development. For Windows user, please setup a Windows Sub-Linux (WSL) environment.
Please ensure to download the correct R version for future development. You can download it from the official CRAN website here: https://cran.r-project.org/bin/macosx/.
For setting up the Python development environment, it is recommended to use virtualenv or conda. These tools help in creating isolated Python environments, ensuring that projects have their own dependencies, regardless of what dependencies every other project has.
We would like to acknowledge WEHI Senior Research Officer Marek Cmero, who wrote the Python script that merges the FACS files together. The relevant file is operations.py which can be found at his repository, and this repository under the scripts directory. For more information, visit the Sister Repository wiki page.
Refer to the GMM Usage wiki page for installing R and RStudio and running the app.
Refer to the GMM Testing wiki page for more information.
Refer to the GMM Deployment wiki page for more information.