This file records changes and additions to the portfolio.
| Date | Section | Description |
|---|---|---|
| 2025-10-27 | Setup | Created repository structure (README, LICENSE, .gitignore, projects/, notebooks/). |
| 2025-10-27 | Projects / Structure | Added initial project templates: Cilia_Module_Validation, LPP_NPP_Heatmap_Visualization, LBS_Consensus_Profiling; added standard .keep files. |
| 2025-10-27 | Project: LPP_NPP_Heatmap_Visualization | Added initial R scripts (gene_list_to_lpp_heatmap.R, gene_list_to_npp_heatmap.R) with full documentation and CLI options. |
| 2025-10-28 | Project: LPP_NPP_Heatmap_Visualization | Added advanced R script lpp_multi_cluster_heatmap_with_inclusion.R for multi-cluster visualization with annotations and full CLI. |
| 2025-10-28 | Project: LPP_NPP_Heatmap_Visualization | Added demo input templates (input/) and example result images (results/NPP_7_genes_HeatMap_2025.png, results/LPP_7_genes_HeatMap_2025.png, results/Clusters_Dominated_by_Known_Genes.png). |
| 2025-10-28 | Project: LPP_NPP_Heatmap_Visualization | Added detailed project README, explaining scripts, inputs, outputs, and embedding example result images. |
| 2025-10-28 | Project: Cilia_Module_Validation | Added 7 Python scripts (extract_cilia_annotations.py to cluster_evidence_viz.py) comprising the complete computational pipeline for cluster analysis (Filter, Enrich, Quantify, Validate, Visualize). |
| 2025-10-28 | Project: Cilia_Module_Validation | Added detailed project README outlining the scientific rationale, the 6-step computational workflow, script descriptions, and usage examples. |
| 2025-10-28 | Project: Cilia_Module_Validation | Added example result images (results/gene_category_distribution_per_cluster.png, results/Clusters_Dominated_by_Known_Genes.png) and embedded them in the README. |
| 2026-06-17 | Project: IRD_Phenotype_Clustering | Replaced empty stub with full synthetic demo (notebook, synthetic gene-HPO matrix, demo figures, updated README). |
| 2026-06-18 | Project: Cilia_Module_Validation | Fixed script filename mismatches, removed orphan stub, corrected broken How to Run example, generalized unpublished quantitative findings. |
| 2026-06-18 | Project: IRD_HPO_Anatomogram | Replaced unredacted real notebooks (01/02) with one self-contained synthetic demo notebook; fixed broken Input/data path mismatch; regenerated gganatogram_organs_input_DEMO.csv from actual demo data; updated README accordingly. |
| 2025-11-24 | Project: LBS_Consensus_Profiling | Added demo notebook (consensus_profile_demo.ipynb) covering five aggregation strategies with coherence validation and noise-based negative control. |
| 2025-11-26 | Project: LBS_Consensus_Profiling | Added project README with scientific rationale, workflow description, and usage instructions. |
| 2026-06-20 | README | Added Repository Structure section with annotated file tree and project overview prose. |
| 2026-06-20 | Housekeeping | Removed internal process documents (PORTFOLIO_GUIDE.md, PORTFOLIO_QUICK_GUIDE.md) not intended for public readers. |