High confidence glycosomal membrane protein inventory unveils trypanosomal Peroxin PEX15

Zenodo DOI: 10.5281/zenodo.14889747

This repository contains data analysis script for the manuscript "High confidence glycosomal membrane protein inventory unveils trypanosomal Peroxin PEX15".

System requirements

• 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 andLICENSE.md R 4.2.2 on MS Windows 10 and Ubuntu 22.04 LTS.

Installation guide

• 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

How to run

• Save and extract the 'txt', 'results' and 'marker_list' folder
• With autoprot installed, run the jupyter notebook 'Tb_PMP_script_data_processing.ipynb'

How to get help

If something does not work as expected, please reach out to us via the GitHub issues function.