This repository contains the data analysis script for the manuscript "p97/VCP is required for piecemeal autophagy of aggresomes"
- Scripts are provided as Jupyter notebooks.
- Analysis was performed using modules from the autoprot project which need to be installed on your local computer
- Autoprot integrates Python and R scripts for proteomics data analysis and therefore requires both languages to be installed
- Software dependencies are detailed in the ''requirements.txt'' file in the autoprot repository
- However, detailed information on all installed packages during execution including version numbers are provided in the respective notebooks (as ''environment.txt'' and ''R_environment.csv'' respectively)
- The scripts were tested with Python 3.10 and R 4.2.2 on MS Windows 10 and Ubuntu 22.04 LTS.
- Install autoprot on your local computer (see installation instructions on the autoprot repository).
- All analyses in this repository were performed with autoprot and cannot be run without it.
- Installation time largely depends on the time required to compile the R packages.
- With a fast internet connection, the installation on a standard desktop computer should take less than 30 minutes.
- No non-standard libraries or hardware are required to run the scripts
- Save and extract the txt folder inside the folder ''data'' -create a 'results' and 'plots' folder
- With autoprot installed, run the jupyter notebooks in numeric order
If something does not work as expected, please reach out to us via the GitHub issues function.