Custom R and Python scripts for the curated gene annotation of Phytophthora plurivora strain TJ71: filtering, heuristic scoring, and figure generation

This repository contains the custom scripts used in the curation, statistical analysis, and figure generation for the high-confidence gene annotation of Phytophthora plurivora strain TJ71, associated with the manuscript "A High-Confidence, Curated Gene Annotation of Phytophthora plurivora Reveals a Two-Speed Genome Architecture and an Expanded Effector Repertoire." Scripts cover repeat- and expression-aware filtering, the heuristic homology-and-topology scoring framework, Spearman correlation analyses between gene/effector density and repeat content, and generation of the manuscript figures. The transcript deduplication script (dedupe_gtf.py) is archived separately at https://doi.org/10.5281/zenodo.21073364.