Assessment of nanopore RNA modification calling in human cell lines and synthetic systems

This repository contains the complete codebase, exemplar datasets, and modkit file used in the study. Each folder includes Jupyter notebooks corresponding to specific figure panels presented in the paper. Each notebook lists the required Python libraries at the beginning, and all analyses require Python 3. All sequence-level data generated in this work are publicly available on AWS (see the paper for access details). All commands used for data processing and analysis are described in detail in the Methods section of the paper.