Resources & downloads
Everything in one place
The whole data-access package — the oryza19k helper and example notebooks, the precomputed tables, and the Supplementary Note — bundled into this site. Grab individual files below, or the complete package as one archive.
⬇ Download everything (.zip) Read Supplementary Note 10 in your browser →
Python — the oryza19k access cookbook
The client-side cookbook that orchestrates every platform (see the API page for what it is and what it needs). import oryza19k as o19, then o19.<function>(...).
| File | What it is | |
|---|---|---|
oryza19k.py | The access-cookbook helper (Ensembl REST, tabix, CLIMtools, models, summaries) | download |
requirements.txt | Library requirements (core + optional groups) | download |
workflow_A_mads14_heading_date.py | Workflow A — MADS14 → heading-date hypothesis | download |
workflow_B_tb1_tiller_number.py | Workflow B — rare TB1/FC1 variant → tiller number | download |
workflow_C_imputation_benchmark.py | Workflow C — whole-collection imputation & benchmarking | download |
README.md | How to run the notebooks; full oryza19k reference | read in browser · .md |
The workflows are jupytext percent-format .py files — valid notebook sources. Convert to .ipynb with jupytext --to notebook workflow_*.py, or run as plain scripts.
Precomputed summary tables
DOI-citable summaries so common questions need no large query (manifest: read in browser · .md). At publication these are mirrored on Zenodo.
| Table | Contents | Size | |
|---|---|---|---|
allele_frequency_core_snps.tsv | 165,640 SNPs × global + per-group allele frequency | ~19 MB | download |
genomic_prediction_benchmark.tsv | 23 models × 5 traits (Spearman, R², training time) | ~13 KB | download |
accession_passport.tsv | accession, varietal group, #phenotypes scored | ~0.4 MB | download |
phenotypes_by_accession.tsv | accession × 24 phenotypes (+ group) | ~1.4 MB | download |
generate_tables.py | Reproducible generator for the tables above | ~8 KB | download |
Documentation
| Document | What it is | |
|---|---|---|
| Supplementary Note 10 | Data Access and Visualization (§§10.1–10.6) | read in browser · .md |
| Package README | Overview of the whole package | read in browser · .md |
Using the .zip: it contains the full site with everything bundled under site/resources/. Unzip, then python -m http.server 8000 --directory site and open http://localhost:8000/.