This repository contains the code for the paper "Estimating protein isoform abundances with PAQu" by Testa et al. (2026), available on biorXiv.
The Python scripts in this repository implement PAQu, the simulation study and the real-data analysis described in the paper. The files are organized as follows:
- PAQu.py: This script contains the routine to run PAQu.
- PAQu_simulations.py: This script implements the main simulation study.
- PAQu_application.py: This script implements the analysis of real-data using PAQu.
- format_upload.py: This script formats the outputs of the PAQu_application.py to make it easier to analyze them.