This is a multi-environment project — different stages used different conda
environments (documented, not a single lockfile). Exact versions for every tool are in hoca_analysis_package_versions.tsv.
| Stage / analysis | Environment spec |
|---|---|
| Integration, benchmark, main scRNA | environment_scib_benchmark.yml, pip_freeze_scib_benchmark.txt, ccc_env.yml |
| scDRS / gsMAP (Fig 5) | environment_requirements_figure5_scdrs_gsmap.txt |
| ORACLE / scGPT (Fig 6) | environment.scgpt.yml, environment.celltypist_gpu.yml |
| R (miloR / limma / edgeR / Seurat) | environment_R_miloR_notes.txt |
| Fig 4 / disease remodelling | ENVIRONMENT_REQUIREMENTS_figure4.md |
| Full per-package version table | hoca_analysis_package_versions.tsv (+ summary .md) |
The minimal Python replot env is environment_python_minimal.yml. Preprocessing-tool
versions (STARsolo 2.7.10a, CellBender 0.3.2, sctk 0.2.4) are recorded in
hoca_analysis_package_versions.tsv.