{
  "generated_at": "2026-07-09 11:31:31 +0800",
  "analysis_scope": "CancerSCEM 2.0 Chinese subset donors with matrix-backed UMAP and expression matrix",
  "samples_completed": 173,
  "failed_samples": 0,
  "programs": [
    "B_plasma",
    "Checkpoint_exhaustion",
    "Endothelial",
    "Epithelial_tumor",
    "Fibroblast_stroma",
    "Myeloid_APC",
    "Proliferation",
    "T_NK_cytotoxic"
  ],
  "tables": {
    "sample_index": "data/human_immune_atlas/analysis/cancerscem_deep/cancerscem_sample_index.tsv",
    "cancer_type_summary": "data/human_immune_atlas/analysis/cancerscem_deep/cancerscem_cancer_type_summary.tsv",
    "program_by_cancer": "data/human_immune_atlas/analysis/cancerscem_deep/cancerscem_program_by_cancer.tsv",
    "top_markers_overall": "data/human_immune_atlas/analysis/cancerscem_deep/cancerscem_top_markers_overall.tsv",
    "top_markers_by_cancer": "data/human_immune_atlas/analysis/cancerscem_deep/cancerscem_top_markers_by_cancer.tsv"
  },
  "charts": [
    {
      "filename": "cancerscem_donors_by_cancer.png",
      "href": "IMG/human-immune-analysis/cancerscem-deep/cancerscem_donors_by_cancer.png",
      "title": "Donors by cancer type"
    },
    {
      "filename": "cancerscem_qc_profile.png",
      "href": "IMG/human-immune-analysis/cancerscem-deep/cancerscem_qc_profile.png",
      "title": "Per-donor QC profile"
    },
    {
      "filename": "cancerscem_program_heatmap.png",
      "href": "IMG/human-immune-analysis/cancerscem-deep/cancerscem_program_heatmap.png",
      "title": "Gene program activity"
    },
    {
      "filename": "cancerscem_cluster_complexity.png",
      "href": "IMG/human-immune-analysis/cancerscem-deep/cancerscem_cluster_complexity.png",
      "title": "Cluster complexity"
    },
    {
      "filename": "cancerscem_recurrent_markers.png",
      "href": "IMG/human-immune-analysis/cancerscem-deep/cancerscem_recurrent_markers.png",
      "title": "Recurrent cluster marker genes"
    }
  ],
  "method": {
    "cell_sampling": "Up to 2000 cells per donor, stratified by existing UMAP clusters.",
    "qc": "Per-cell UMI, detected-gene, and mitochondrial percent summaries from count matrices.",
    "markers": "Top cluster marker genes ranked by mean log1p cluster-vs-rest difference.",
    "programs": "Eight fixed immune, stromal, epithelial, proliferation, and checkpoint gene programs."
  }
}