MoschouLab/pbody-proteomics-meta-analysis-pipeline: v1.0.1 - Initial Public Release

Tag: v1.0.1 Target: main Title: v1.0.1 - Initial Public Release (Zenodo Integration) Description: P-body Proteomics Meta-Analysis Pipeline v1.0.1 Initial public release of the reproducible bioinformatics pipeline for P-body proteomics meta-analysis. 📊 Pipeline Components Script 01: Data loading and quality control (4,774 proteins) Script 02: UniProt annotation enrichment (99.79% annotated) Script 03: Cell wall enrichment analysis (Fisher's exact test) Script 04: Comprehensive GO enrichment (1,277 terms tested) Script 05: Venn/UpSet overlap analysis (12 intersections, PPI network) 📈 Key Results Total enriched genes: 1,095 Core P-body gene (all 4 conditions): 1 (AT1G08370) Significant GO terms: 104 (FDR < 0.05) Network coherence: 2.4-3.0 (highly interconnected) 🔬 Associated Publication Analysis supports the review manuscript: Moschou, P.N., et al. (in preparation). "Cell Wall Dynamics and Biomolecular Condensates in Plants." Input data from: Liu C, et al. (2023). An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome. EMBO J. 42(9):e111885. DOI: 10.15252/embj.2022111885 👥 Authors Moya-Cuevas J (Lead Bioinformatics Scientist) Moschou PN (Principal Investigator) Institution: University of Crete, Institute of Molecular Biology and Biotechnology Project: PLANTEX ERC Consolidator Grant 🐍 System Requirements Python 3.10 8 GB RAM minimum Linux/macOS (tested on Ubuntu 24.04) 📦 Installation git clone https://github.com/MoschouLab/pbody-proteomics-meta-analysis-pipeline.git cd pbody-proteomics-meta-analysis-pipeline conda env create -f environment.yml conda activate pbody_proteomics 🚀 Quick Start python scripts/01_load_pbody_proteomics.py python scripts/02_fetch_protein_annotations.py python scripts/03_cell_wall_enrichment_analysis.py python scripts/04_go_enrichment_comprehensive.py --threshold 0.8 python scripts/05_venn_upset_analysis.py --threshold 0.8 --bootstraps 1000 📄 License MIT License - See LICENSE file 🔗 Links Documentation: See README.md Issues: Report bugs DOI: Will be assigned by Zenodo upon release publication Note: This is a re-release to trigger Zenodo DOI assignment. Functionally identical to v1.0.0.