| # Parse PBMC cytokine: 18 cell types x 12 donors x ~100 cytokines | |
| # Each h5ad file is one cell type with all donors and cytokines. | |
| # Pseudobulk is computed per (donor, cytokine) within each cell type, | |
| # with PBS as the control condition. | |
| dataset: parse | |
| h5ad_dir: /nvme-shared/Data/parse_pbmc/by_cell_type | |
| h5ad_pattern: "*.h5ad" | |
| treatment_col: cytokine | |
| control: PBS | |
| # Within each h5ad (one cell type), stratify by donor. | |
| group_col: donor | |
| # The cell type identity comes from the filename — carry it in output. | |
| file_id_col: cell_type | |
| pdex: | |
| output_dir: /nvme-shared/Data/parse_pbmc/by_cell_type/pdex_results | |
| threads: 24 | |
| n_workers: 8 # parallel workers over group_col values | |
| celleval: | |
| output_dir: /nvme-shared/Data/parse_pbmc/by_cell_type/delta_results | |
| gene_mode: all_genes | |
| gene_name_col: null # use var.index | |
| target_sum: 3320 # dataset-wide median transcript count | |