Archive 4 checkpoints (1-4)

paper-releases/20260928/diffusion/data/cohorts/imperial_eskd/samples.csv

@@ -0,0 +1,173 @@
+row,sample_id,donor_id,group,n_cells
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+128,C167_1205,C167,covid_negative,9978
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+138,C169_2301,C169,covid_positive,3773
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+141,C170_1205,C170,covid_negative,953
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+143,C170_0202,C170,covid_positive,5621
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+145,C170_0403,C170,recovery,3745
+146,C187_2605,C187,covid_negative,1867
+147,C187_1201,C187,covid_positive,1985
+148,C187_1401,C187,covid_positive,3155
+149,C187_1901,C187,covid_positive,1966
+150,C187_2301,C187,covid_positive,529
+151,C187_2502,C187,recovery,5693
+152,C190_2605,C190,covid_negative,1791
+153,C190_2901,C190,covid_positive,1527
+154,C190_0102,C190,covid_positive,4868
+155,C190_0302,C190,covid_positive,2220
+156,C190_0502,C190,covid_positive,2030
+157,C190_0802,C190,covid_positive,1447
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+160,C193_2605,C193,covid_negative,5566
+161,C195_2605,C195,covid_negative,7759
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+165,C224_2805,C224,covid_negative,6721
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+167,C237_2805,C237,covid_negative,5071
+168,C238_2905,C238,covid_negative,7843
+169,C240_2905,C240,covid_negative,2346
+170,C246_2905,C246,covid_negative,769
+171,C251_2905,C251,covid_negative,2117

paper-releases/20260928/diffusion/data/cohorts/ji2025_chili/MANIFEST.json

@@ -0,0 +1,1150 @@
+{
+ "schema": "ji2025_chili_paired_ft_v1",
+ "written_utc": "2026-09-28T02:54:54.037476+00:00",
+ "started_utc": "2026-09-28T02:54:32.131761+00:00",
+ "study": "Ji C et al., Cancer Immunol Immunother 2025 (PMC12049347; NCT04476563); bulk GSE287540, scRNA GSE287541",
+ "rows": 40,
+ "row_order": "bulk GSM ascending",
+ "patients": 23,
+ "pairs_by_timepoint": {
+  "AC": 13,
+  "TOL": 10,
+  "BC": 9,
+  "FU1": 8
+ },
+ "pairs_by_outcome": {
+  "control": 22,
+  "ChILI": 18
+ },
+ "pairs_by_outcome_timepoint": {
+  "control_AC": 13,
+  "ChILI_TOL": 10,
+  "control_BC": 9,
+  "ChILI_FU1": 8
+ },
+ "pairs_per_patient": {
+  "N064": 2,
+  "N032": 2,
+  "N022": 2,
+  "N018": 2,
+  "N012": 2,
+  "N005": 2,
+  "N002": 2,
+  "N001": 2,
+  "N159": 2,
+  "N158": 2,
+  "N150": 2,
+  "N043": 2,
+  "N129": 2,
+  "N128": 2,
+  "N138": 2,
+  "N136": 2,
+  "N038": 2,
+  "N087": 1,
+  "N106": 1,
+  "N063": 1,
+  "N055": 1,
+  "N035": 1,
+  "N147": 1
+ },
+ "pairs_by_id_match": {
+  "exact_subject_id": 39,
+  "zero_padding_difference": 1
+ },
+ "cells": {
+  "n_cells": 154698,
+  "nnz": 56967893,
+  "per_row_min": 759,
+  "per_row_median": 3585.5,
+  "per_row_max": 8987,
+  "author_filtered_cells_in_paired_libraries": 155718
+ },
+ "retained_cells_rule": "flag_conservative_review_pass = genes>=200 & UMIs>=500 & mito<=20% (qc_core, ImMicro definition) applied to the author-filtered Seurat cells; MAD flags are review-only columns",
+ "features_semantics": {
+  "bulk_raw": "Salmon 1.10.0 gene-level estimated read counts (QuantSeq 3' FWD, PAXgene WHOLE BLOOD) on the canonical axis, float64 exactly as deposited (never rounded; the deposited table happens to be integer-valued); 0 where bulk_valid is False",
+  "pseudo_raw_sum": "sum of retained cells' UMI counts (Seurat RNA@counts) on the canonical axis; storage 0 where sc_valid is False",
+  "bulk_valid": "harmonization_valid from qc_bulk.harmonize (gene in the Salmon table, unique mapping)",
+  "sc_valid": "harmonization_valid from qc_singlecell.canonical_export (gene in the CellRanger 2020-A feature table)",
+  "pair_valid": "bulk_valid & sc_valid",
+  "sample_ids": "<patient>_<timepoint>, e.g. N022_TOL",
+  "donor_ids": "patient (N###, zero-padded)",
+  "groups": "= timepoints: GEO time label BC (before ICI), AC (control patients ~12 weeks after ICI start), TOL (time of liver injury), FU1 (follow-up 3-49 d after TOL)",
+  "outcome": "GEO group: ChILI or control (ICI-treated, no ChILI)",
+  "extra_keys": "timepoints, outcome, bulk_gsm, sc_gsm, sc_title_sample_id (=PID_visit), id_match, bulk_title, sc_title, bulk_library, sc_library_key, bulk_batch, sc_round, sex_geo, age_geo, age_geo_bulk, regimen, cancer_type, steroid_bulk, steroid_sc, identity_pass, identity_check, sex_bulk_expr, sex_sc_expr"
+ },
+ "specimen_warning": "The bulk RNA is from PAXgene WHOLE BLOOD (GEO extract protocol and paper methods), not PBMC; the sc data are PBMC (dead-cell removed). Same patient and same visit, different specimen. Whole blood contains neutrophils and reticulocyte globin RNA that PBMC lack.",
+ "specimen_evidence_median_cpm": {
+  "hemoglobin:HBB": {
+   "bulk_median_cpm_paired": 45935.13745369274,
+   "sc_median_cpm_paired": 11.187359611646025
+  },
+  "hemoglobin:HBA1": {
+   "bulk_median_cpm_paired": 12567.605367951628,
+   "sc_median_cpm_paired": 0.47994615929587714
+  },
+  "hemoglobin:HBA2": {
+   "bulk_median_cpm_paired": 59214.854066825836,
+   "sc_median_cpm_paired": 0.451562324121646
+  },
+  "hemoglobin:HBD": {
+   "bulk_median_cpm_paired": 202.9409864471506,
+   "sc_median_cpm_paired": 2.212753373207536
+  },
+  "neutrophil:FCGR3B": {
+   "bulk_median_cpm_paired": 1998.5756846141126,
+   "sc_median_cpm_paired": 1.7978031347076113
+  },
+  "neutrophil:CXCR2": {
+   "bulk_median_cpm_paired": 1118.9921204749648,
+   "sc_median_cpm_paired": 3.4305534172705316
+  },
+  "neutrophil:CSF3R": {
+   "bulk_median_cpm_paired": 1533.2063960727462,
+   "sc_median_cpm_paired": 94.94418679068605
+  },
+  "neutrophil:MMP9": {
+   "bulk_median_cpm_paired": 178.7711505592709,
+   "sc_median_cpm_paired": 1.79655299055965
+  },
+  "neutrophil:CAMP": {
+   "bulk_median_cpm_paired": 69.45231692382592,
+   "sc_median_cpm_paired": 0.6383841257501319
+  },
+  "neutrophil:LTF": {
+   "bulk_median_cpm_paired": 54.014991601841,
+   "sc_median_cpm_paired": 0.0
+  },
+  "lymphocyte:CD3E": {
+   "bulk_median_cpm_paired": 38.319131826098214,
+   "sc_median_cpm_paired": 589.8042027203924
+  },
+  "lymphocyte:MS4A1": {
+   "bulk_median_cpm_paired": 49.665057369773116,
+   "sc_median_cpm_paired": 46.01327714049776
+  },
+  "lymphocyte:IL7R": {
+   "bulk_median_cpm_paired": 476.3330557497402,
+   "sc_median_cpm_paired": 400.91362513398735
+  },
+  "monocyte:CD14": {
+   "bulk_median_cpm_paired": 235.32824957613377,
+   "sc_median_cpm_paired": 214.24915908549315
+  },
+  "monocyte:LYZ": {
+   "bulk_median_cpm_paired": 2600.249717301701,
+   "sc_median_cpm_paired": 1369.2013878279033
+  },
+  "hemoglobin_fraction_of_canonical_bulk_counts_paired": {
+   "median": 0.12602329223836908,
+   "min": 0.03953196011681557,
+   "max": 0.25913359692739013
+  },
+  "hemoglobin_fraction_of_canonical_sc_counts_paired": {
+   "median": 1.4618499197358798e-05
+  }
+ },
+ "identity": {
+  "sex_rule": "CPM on the source axis (bulk: Salmon table; sc: retained cells, all RNA features); score=log2(XIST+1)-log2(RPS4Y1+DDX3Y+UTY+KDM5D+1); female>2, male<-2, else ambiguous; opposite-sex signal flag: female call with Y CPM>20 or male call with XIST CPM>50 (bulk)",
+  "genes": "19126 canonical genes measured in all 128 bulks and all 46 sc libraries, chrY excluded; 8167 'expressed' (bulk mean log2CPM>3 and sc mean>1)",
+  "expression_rule_as_ye": "Spearman over the top 2000 genes by mean log2(CPM+1), each paired bulk vs all 46 sc pseudobulks; centred and reverse variants",
+  "expression_residualised_rule": "within each modality centre log2(CPM+1), remove the top k sample PCs (computed on expressed genes), keep the 2000 genes with the highest residual variance in both modalities (rank sum), Pearson all 128 bulks x all 46 sc libraries. Primary k=5 (~10% of the 46 sc libraries; Ye used 10 for 133/207); sensitivity k=[0, 3, 5, 8, 10]. Uses no pairing information.",
+  "verdict_rule": "pass = sex concordant (bulk, sc, GEO) and at k=5 the own PATIENT ranked 1st in one direction and <=5th in the other (candidates collapsed to patients by their best r: 28 sc patients, 61 bulk patients); fail = sex discordant or own patient >5th in both directions; else borderline",
+  "discrimination_by_k": {
+   "0": {
+    "n_genes_selected": 2000,
+    "pairs_own_library_top1_bulk_to_sc": 20,
+    "pairs_own_library_top1_sc_to_bulk": 11,
+    "pairs_own_patient_top1_bulk_to_sc": 24,
+    "pairs_own_patient_top1_sc_to_bulk": 16,
+    "all_bulks_top_sc_same_patient": "26/55",
+    "all_bulks_chance_rate": 0.0387,
+    "all_sc_top_bulk_same_patient": "16/42",
+    "all_sc_chance_rate": 0.0182,
+    "auc_same_patient_vs_other_patient_all_bulk_sc_combinations": 0.8178315885939869,
+    "median_r_paired": 0.26420639720561123,
+    "median_r_same_patient_other_timepoint": 0.12441825073369689,
+    "median_r_other_patient": -0.0027965909541629906,
+    "p99_r_other_patient": 0.3316049653388173,
+    "timepoint_own_best_within_patient_bulk_to_sc": "25/34",
+    "timepoint_own_best_within_patient_sc_to_bulk": "29/39"
+   },
+   "3": {
+    "n_genes_selected": 2000,
+    "pairs_own_library_top1_bulk_to_sc": 28,
+    "pairs_own_library_top1_sc_to_bulk": 22,
+    "pairs_own_patient_top1_bulk_to_sc": 36,
+    "pairs_own_patient_top1_sc_to_bulk": 30,
+    "all_bulks_top_sc_same_patient": "41/55",
+    "all_bulks_chance_rate": 0.0387,
+    "all_sc_top_bulk_same_patient": "30/42",
+    "all_sc_chance_rate": 0.0182,
+    "auc_same_patient_vs_other_patient_all_bulk_sc_combinations": 0.882527933453174,
+    "median_r_paired": 0.21384325155764486,
+    "median_r_same_patient_other_timepoint": 0.12609740081962167,
+    "median_r_other_patient": -0.0018853255422834618,
+    "p99_r_other_patient": 0.1798317994848483,
+    "timepoint_own_best_within_patient_bulk_to_sc": "26/34",
+    "timepoint_own_best_within_patient_sc_to_bulk": "28/39"
+   },
+   "5": {
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+    "pairs_own_library_top1_bulk_to_sc": 26,
+    "pairs_own_library_top1_sc_to_bulk": 16,
+    "pairs_own_patient_top1_bulk_to_sc": 34,
+    "pairs_own_patient_top1_sc_to_bulk": 24,
+    "all_bulks_top_sc_same_patient": "41/55",
+    "all_bulks_chance_rate": 0.0387,
+    "all_sc_top_bulk_same_patient": "24/42",
+    "all_sc_chance_rate": 0.0182,
+    "auc_same_patient_vs_other_patient_all_bulk_sc_combinations": 0.9012759507948257,
+    "median_r_paired": 0.172525567467166,
+    "median_r_same_patient_other_timepoint": 0.10176401191443879,
+    "median_r_other_patient": -0.002668921487922646,
+    "p99_r_other_patient": 0.14572437507183672,
+    "timepoint_own_best_within_patient_bulk_to_sc": "24/34",
+    "timepoint_own_best_within_patient_sc_to_bulk": "26/39"
+   },
+   "8": {
+    "n_genes_selected": 2000,
+    "pairs_own_library_top1_bulk_to_sc": 28,
+    "pairs_own_library_top1_sc_to_bulk": 22,
+    "pairs_own_patient_top1_bulk_to_sc": 35,
+    "pairs_own_patient_top1_sc_to_bulk": 27,
+    "all_bulks_top_sc_same_patient": "38/55",
+    "all_bulks_chance_rate": 0.0387,
+    "all_sc_top_bulk_same_patient": "27/42",
+    "all_sc_chance_rate": 0.0182,
+    "auc_same_patient_vs_other_patient_all_bulk_sc_combinations": 0.9333350956963096,
+    "median_r_paired": 0.1473420491268157,
+    "median_r_same_patient_other_timepoint": 0.09352613438723947,
+    "median_r_other_patient": -0.0027321462024837264,
+    "p99_r_other_patient": 0.111222314620384,
+    "timepoint_own_best_within_patient_bulk_to_sc": "24/34",
+    "timepoint_own_best_within_patient_sc_to_bulk": "28/39"
+   },
+   "10": {
+    "n_genes_selected": 2000,
+    "pairs_own_library_top1_bulk_to_sc": 30,
+    "pairs_own_library_top1_sc_to_bulk": 19,
+    "pairs_own_patient_top1_bulk_to_sc": 34,
+    "pairs_own_patient_top1_sc_to_bulk": 26,
+    "all_bulks_top_sc_same_patient": "40/55",
+    "all_bulks_chance_rate": 0.0387,
+    "all_sc_top_bulk_same_patient": "27/42",
+    "all_sc_chance_rate": 0.0182,
+    "auc_same_patient_vs_other_patient_all_bulk_sc_combinations": 0.9297204892319623,
+    "median_r_paired": 0.1305960761110332,
+    "median_r_same_patient_other_timepoint": 0.08878331380592318,
+    "median_r_other_patient": -0.0018538108455484668,
+    "p99_r_other_patient": 0.0998767853077794,
+    "timepoint_own_best_within_patient_bulk_to_sc": "26/34",
+    "timepoint_own_best_within_patient_sc_to_bulk": "26/39"
+   }
+  },
+  "anomaly_probe_N127_N131": {
+   "Rd4a_N131V01": {
+    "top_bulk": [
+     [
+      "N128_control_AC",
+      0.157
+     ],
+     [
+      "N128_control_BC",
+      0.143
+     ],
+     [
+      "N002_chili_FU1",
+      0.142
+     ]
+    ],
+    "r_bulk_N131_chili_BC": 0.11573928198320502
+   },
+   "Rd4a_N127V00": {
+    "top_bulk": [
+     [
+      "N022_chili_BC",
+      0.089
+     ],
+     [
+      "N131_chili_BC",
+      0.089
+     ],
+     [
+      "N002_chili_FU1",
+      0.075
+     ]
+    ],
+    "r_bulk_N131_chili_BC": 0.08853588467416963
+   },
+   "Rd5_N131V01": {
+    "top_bulk": [
+     [
+      "N002_chili_FU1",
+      0.171
+     ],
+     [
+      "N111_chili_TOL",
+      0.159
+     ],
+     [
+      "N128_control_AC",
+      0.156
+     ]
+    ],
+    "r_bulk_N131_chili_BC": 0.08534111701607132
+   },
+   "sc_sc_residual_pearson": {
+    "Rd4a_N131V01~Rd4a_N127V00": -0.0008839730186935551,
+    "Rd4a_N131V01~Rd5_N131V01": 0.6998035126101093,
+    "Rd4a_N127V00~Rd5_N131V01": -0.07732433465209723
+   },
+   "sc_sc_reference": {
+    "different_patients_median": -0.031381265771224576,
+    "different_patients_p99": 0.31653969303897717,
+    "same_patient_other_patients_median": 0.3609033317581365,
+    "same_patient_min": -0.016453533788050125
+   }
+  },
+  "policy": "reported only; no row dropped on identity results; features.npz carries identity_pass / identity_check"
+ },
+ "checks": {
+  "gene_positions_sha256_ok": true,
+  "panel_gene_ids_match_selected_genes_csv": true,
+  "bulk_finite_nonnegative_inside_mask": true,
+  "bulk_fractional_values_inside_mask": 0,
+  "pseudo_raw_sum_equals_sum_of_retained_cells_full_axis": true,
+  "cells_panel_sums_equal_pseudo_raw_sum_positions_exactly": true,
+  "cells_per_row_equal_qc_cell_counts": true,
+  "no_sc_mass_outside_sc_valid": true,
+  "one_sample_id_per_library": true,
+  "sex_concordant_pairs": "40/40",
+  "sex_discordant_bulk_all": [
+   "N106_control_BC",
+   "N87_control_BC",
+   "N086_chili_BC",
+   "N96_control_AC",
+   "N141_control_BC",
+   "N141_control_AC",
+   "N143_control_BC",
+   "N143_control_AC",
+   "N146_control_BC",
+   "N146_control_AC"
+  ],
+  "sex_discordant_sc_all": [],
+  "expression_best_match_is_own_pair": "4/40",
+  "expression_best_match_is_own_pair_centred": "11/40",
+  "expression_reverse_best_match_is_own_pair": "0/40",
+  "identity_check_pass": "33/40",
+  "identity_check_fail": [
+   "N087_AC",
+   "N158_BC"
+  ],
+  "identity_check_borderline": [
+   "N032_BC",
+   "N063_AC",
+   "N106_AC",
+   "N150_AC",
+   "N159_AC"
+  ]
+ },
+ "excluded": {
+  "quarantined_sc_libraries_among_pairs": [],
+  "sc_libraries_without_bulk": [
+   {
+    "sc_gsm": "GSM8747412",
+    "library_key": "Rd1_N014V01",
+    "sample_id": "N014_BC",
+    "unpaired_reason": "no bulk for N014 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
+   },
+   {
+    "sc_gsm": "GSM8747414",
+    "library_key": "Rd1_N016V01",
+    "sample_id": "N016_BC",
+    "unpaired_reason": "no bulk for N016 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
+   },
+   {
+    "sc_gsm": "GSM8747422",
+    "library_key": "Rd1_N037V01",
+    "sample_id": "N037_BC",
+    "unpaired_reason": "no bulk for N037 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
+   },
+   {
+    "sc_gsm": "GSM8747460",
+    "library_key": "Rd4a_N131V01",
+    "sample_id": "N131_TOL",
+    "unpaired_reason": "no bulk for N131 at TOL; bulk timepoints of this patient: BC"
+   },
+   {
+    "sc_gsm": "GSM8747462",
+    "library_key": "Rd4a_N127V00",
+    "sample_id": "N127_BC",
+    "unpaired_reason": "no bulk for N127 at BC; bulk timepoints of this patient: none (patient absent from GSE287540)"
+   },
+   {
+    "sc_gsm": "GSM8747488",
+    "library_key": "Rd5_N131V01",
+    "sample_id": "N131_TOL",
+    "unpaired_reason": "no bulk for N131 at TOL; bulk timepoints of this patient: BC"
+   }
+  ],
+  "bulk_samples_without_sc": [
+   {
+    "gsm": "GSM8747284",
+    "Sample_title": "N064_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: FU1,TOL"
+   },
+   {
+    "gsm": "GSM8747287",
+    "Sample_title": "N064_chili_FU2",
+    "ch_time": "FU2",
+    "reason": "no sc library at FU2; sc timepoints of this patient: FU1,TOL"
+   },
+   {
+    "gsm": "GSM8747288",
+    "Sample_title": "N072_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747289",
+    "Sample_title": "N072_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747290",
+    "Sample_title": "N073_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747291",
+    "Sample_title": "N073_chili_FU1",
+    "ch_time": "FU1",
+    "reason": "no sc library at FU1; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747292",
+    "Sample_title": "N078_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747293",
+    "Sample_title": "N078_chili_FU1",
+    "ch_time": "FU1",
+    "reason": "no sc library at FU1; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747294",
+    "Sample_title": "N002_chili_FU2",
+    "ch_time": "FU2",
+    "reason": "no sc library at FU2; sc timepoints of this patient: FU1,TOL"
+   },
+   {
+    "gsm": "GSM8747295",
+    "Sample_title": "N012_chili_FU2",
+    "ch_time": "FU2",
+    "reason": "no sc library at FU2; sc timepoints of this patient: FU1,TOL"
+   },
+   {
+    "gsm": "GSM8747296",
+    "Sample_title": "N022_chili_FU2",
+    "ch_time": "FU2",
+    "reason": "no sc library at FU2; sc timepoints of this patient: FU1,TOL"
+   },
+   {
+    "gsm": "GSM8747297",
+    "Sample_title": "N043_chili_FU2",
+    "ch_time": "FU2",
+    "reason": "no sc library at FU2; sc timepoints of this patient: FU1,TOL"
+   },
+   {
+    "gsm": "GSM8747302",
+    "Sample_title": "N050_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747303",
+    "Sample_title": "N050_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747304",
+    "Sample_title": "N055_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: AC"
+   },
+   {
+    "gsm": "GSM8747306",
+    "Sample_title": "N063_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: AC"
+   },
+   {
+    "gsm": "GSM8747308",
+    "Sample_title": "N101_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747309",
+    "Sample_title": "N100_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747311",
+    "Sample_title": "N111_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747312",
+    "Sample_title": "N106_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: AC"
+   },
+   {
+    "gsm": "GSM8747313",
+    "Sample_title": "N113_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747314",
+    "Sample_title": "N96_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747316",
+    "Sample_title": "N87_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: AC"
+   },
+   {
+    "gsm": "GSM8747317",
+    "Sample_title": "N086_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747318",
+    "Sample_title": "N96_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747319",
+    "Sample_title": "N101_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747320",
+    "Sample_title": "N111_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747321",
+    "Sample_title": "N117_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747322",
+    "Sample_title": "N117_chili_FU1",
+    "ch_time": "FU1",
+    "reason": "no sc library at FU1; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747323",
+    "Sample_title": "N117_chili_FU2",
+    "ch_time": "FU2",
+    "reason": "no sc library at FU2; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747324",
+    "Sample_title": "N119_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747325",
+    "Sample_title": "N119_chili_FU1",
+    "ch_time": "FU1",
+    "reason": "no sc library at FU1; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747326",
+    "Sample_title": "N119_chili_FU2",
+    "ch_time": "FU2",
+    "reason": "no sc library at FU2; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747327",
+    "Sample_title": "N132_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747328",
+    "Sample_title": "N131_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: TOL,TOL"
+   },
+   {
+    "gsm": "GSM8747329",
+    "Sample_title": "N132_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747330",
+    "Sample_title": "N132_chili_FU1",
+    "ch_time": "FU1",
+    "reason": "no sc library at FU1; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747335",
+    "Sample_title": "N112_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747336",
+    "Sample_title": "N112_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747337",
+    "Sample_title": "N120_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747338",
+    "Sample_title": "N120_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747339",
+    "Sample_title": "N121_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747340",
+    "Sample_title": "N121_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747341",
+    "Sample_title": "N122_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747342",
+    "Sample_title": "N122_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747348",
+    "Sample_title": "N154_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747349",
+    "Sample_title": "N162_chili_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747350",
+    "Sample_title": "N162_chili_TOL",
+    "ch_time": "TOL",
+    "reason": "no sc library at TOL; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747351",
+    "Sample_title": "N133_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747352",
+    "Sample_title": "N133_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747353",
+    "Sample_title": "N137_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747354",
+    "Sample_title": "N137_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747355",
+    "Sample_title": "N141_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747356",
+    "Sample_title": "N141_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747357",
+    "Sample_title": "N143_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747358",
+    "Sample_title": "N143_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747359",
+    "Sample_title": "N146_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747360",
+    "Sample_title": "N146_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747361",
+    "Sample_title": "N149_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747362",
+    "Sample_title": "N149_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747373",
+    "Sample_title": "N003_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747374",
+    "Sample_title": "N003_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747377",
+    "Sample_title": "N007_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747378",
+    "Sample_title": "N007_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747379",
+    "Sample_title": "N010_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747380",
+    "Sample_title": "N010_control_AC",
+    "ch_time": "AC",
+    "reason": "no sc library at AC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747383",
+    "Sample_title": "N013_control_BC",
+    "ch_time": "BC",
+    "reason": "no sc library at BC; sc timepoints of this patient: none (patient absent from GSE287541)"
+   },
+   {
+    "gsm": "GSM8747384",
+    "Sample_title": "N013_control_AC",
+    "ch_time": "AC",
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paper-releases/20260928/diffusion/data/cohorts/ji2025_chili/PREPARE.json

@@ -0,0 +1,101 @@
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+  "fold2/test_raw.npz": "d9a1eb82edf9f6a2ccd110049a18740554ca1d2b02f4ff331a12e7eb7207a7c6",
+  "fold2/test_cal.npz": "35a5ff5b253edc7c615b68b1626c014b53b22c2e19677e359d7a22df0ea5c424",
+  "fold2/test_pseudo.npz": "b0860df9c0976caee7d609dc9323b6b02c57cc72f88e2771064bdd894210fb3d",
+  "fold3/conditions_cal_fixed.npz": "fd40e1bc883d29312e09af291003c6dd9fa7576f92f8499e49cf4f3e88765e34",
+  "fold3/test_raw.npz": "88966294fba326c89d09132dae241ca7b2a512437226aef627ba546fcc740b62",
+  "fold3/test_cal.npz": "7b41346a5e03e6818d2e3a0b6d40b9f9926ccac0badabe97543c7fed15fca4bf",
+  "fold3/test_pseudo.npz": "a0d9743a08d5e098c66761f06527929384053e0ed24bbe234b77a52b3058a6e4",
+  "fold4/conditions_cal_fixed.npz": "13c4b1ef7ba11de48b029ab842a6b6c83aba9c07c35dcdba3692e22470720c27",
+  "fold4/test_raw.npz": "bf199c7e5d1d10f0ebd25b20bc35ad35cf64987bd703019896682b4e87f04302",
+  "fold4/test_cal.npz": "7c4b5095b722829f844a50b40ea11f8d6500b10f2a70bd9023e29b9665484429",
+  "fold4/test_pseudo.npz": "7cee8d86551a81b873ffaa2e304a9b4cbd9d3593d9157318842c7a533db0f65f"
+ },
+ "fold_sizes": {
+  "0": {
+   "test": 7,
+   "train": 23,
+   "inner_val": 3,
+   "test_groups": {
+    "TOL": 2,
+    "FU1": 2,
+    "AC": 2,
+    "BC": 1
+   },
+   "alpha_genes_estimated": 11163
+  },
+  "1": {
+   "test": 6,
+   "train": 23,
+   "inner_val": 4,
+   "test_groups": {
+    "AC": 2,
+    "TOL": 2,
+    "BC": 1,
+    "FU1": 1
+   },
+   "alpha_genes_estimated": 11178
+  },
+  "2": {
+   "test": 6,
+   "train": 24,
+   "inner_val": 3,
+   "test_groups": {
+    "TOL": 2,
+    "FU1": 2,
+    "AC": 1,
+    "BC": 1
+   },
+   "alpha_genes_estimated": 11185
+  },
+  "3": {
+   "test": 8,
+   "train": 22,
+   "inner_val": 3,
+   "test_groups": {
+    "TOL": 2,
+    "FU1": 2,
+    "BC": 2,
+    "AC": 2
+   },
+   "alpha_genes_estimated": 11158
+  },
+  "4": {
+   "test": 6,
+   "train": 24,
+   "inner_val": 3,
+   "test_groups": {
+    "TOL": 2,
+    "BC": 2,
+    "FU1": 1,
+    "AC": 1
+   },
+   "alpha_genes_estimated": 11166
+  }
+ },
+ "checks": {}
+}

paper-releases/20260928/diffusion/data/cohorts/ji2025_chili/QC_REPORT.md

@@ -0,0 +1,139 @@
+# Ji 2025 ChILI: paired bulk and scRNA (QC report)
+
+Study: Ji C et al., Cancer Immunol Immunother 2025 (PMC12049347). The patients developed liver injury on checkpoint inhibitors (ChILI) or were ICI-treated controls. Bulk is GEO GSE287540 and scRNA is GSE287541.
+Built 2026-09-28 on server_1, CPU only. Processing directory: `/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/`.
+
+## Read this first: the bulk is whole blood, not PBMC
+
+The GEO extract protocol and the paper's methods both say the bulk RNA came from **PAXgene whole-blood tubes**. The abstract says "PBMC". The data agree with the methods:
+
+- Hemoglobin genes are a median 12.6% of bulk counts (range 4 to 26%), against 0.001% in the sc pseudobulk.
+- Neutrophil genes are high in bulk and near zero in sc: FCGR3B is 1,999 vs 1.8 CPM and CXCR2 is 1,119 vs 3.4 CPM.
+
+So a pair is the same patient at the same visit, but a different specimen. The sc data are PBMC with dead cells removed. A bulk-to-PBMC model will see neutrophil and globin signal that no PBMC cell can explain.
+
+## Result
+
+**40 pairs from 23 patients** (17 patients have 2 pairs, 6 have 1). **33 pass** the identity checks, **5 are borderline** and **2 fail**. Every row is kept. `identity_pass` is True only for pass, as in Ye 2026. With that flag, `prepare_dataset.py` uses 33 rows from 20 patients.
+
+| timepoint | meaning | pairs | outcome | retained cells per sample, median (min to max) |
+|---|---|---|---|---|
+| BC | before checkpoint inhibitor | 9 | all control | 3,087 (1,780 to 6,359) |
+| AC | control patients, about 12 weeks after the first dose | 13 | all control | 3,749 (1,632 to 8,987) |
+| TOL | time of liver injury | 10 | all ChILI | 3,431 (759 to 6,709) |
+| FU1 | follow-up, 3 to 49 days after TOL | 8 | all ChILI | 3,903 (2,107 to 4,975) |
+| all | | 40 | 22 control, 18 ChILI | 3,586 (759 to 8,987); 154,698 cells in total |
+
+In these pairs, the timepoint fully determines the outcome. No ChILI patient has a paired BC: the four ChILI BC sc libraries have no bulk. So `groups` (= timepoint) also encodes case versus control. No FU2 sc library exists.
+
+The earlier search expected 39 pairs. The 40th is **N087_AC**: bulk writes the ID as `N87` and sc as `N087`. It is marked `id_match = zero_padding_difference`. It is also one of the two identity failures.
+
+## Pairing rule
+
+- Pair = same patient AND same GEO `time` label. Patient IDs are zero-padded to three digits. Timepoint is the GEO field; for sc it also equals the per-cell Seurat `Time`.
+- An accepted pair must agree on GEO sex, outcome group and ICI regimen, and on age within 1 year. All 40 agree.
+- Differences are recorded but not refused: N128_AC and N129_AC differ in age by 1 year, and N043_TOL has steroid `n` in bulk and `y` in sc.
+- The 46 TCR GSMs are V(D)J libraries and are not paired.
+
+**Not paired** (full lists in MANIFEST.json `excluded` and in `processing/.../pairing/`):
+
+- 6 sc libraries have no bulk:
+  - N014_BC, N016_BC, N037_BC and N127_BC: these patients are not in the bulk series.
+  - N131_TOL has two libraries (Rd4a and Rd5), but bulk has N131 only at BC.
+- 88 bulk samples have no sc: 39 BC, 24 AC, 12 TOL, 6 FU1 and 7 FU2.
+
+## Identity checks
+
+**Sex.** Rule as in Ye 2026: XIST against RPS4Y1 + DDX3Y + UTY + KDM5D, in source-axis CPM.
+
+- All 40 pairs agree across bulk, sc and GEO. All 46 sc libraries agree with GEO.
+- **10 of 128 bulk samples disagree with GEO sex.** None is a paired bulk. They sit in two sequencing batches:
+  - Batch 3 (4 of 11): N106_control_BC, N87_control_BC, N086_chili_BC and N96_control_AC. These look like swapped labels.
+  - Batch 5 (6 of 22): N141 and N143 (GEO female, both samples male) and N146 (GEO male, both samples female). These look like wrong sex labels or a block swap.
+- Treat every batch 3 and batch 5 bulk as less certain. Of the 7 non-passing pairs, 5 use batch 3 or 5 bulks.
+
+**Expression, as in Ye.** Spearman over the top 2,000 genes by mean: only 4 of 40 bulks pick their own sc. This test tracks specimen type and composition, not the donor.
+
+**Expression, donor-sensitive.** This test decides pass or fail. It uses no pairing information.
+
+- Genes: 19,126 genes measured in all 128 bulks and all 46 sc libraries. chrY genes are excluded so this test is independent of the sex check.
+- Method: within each modality, remove the top k sample PCs. Keep the 2,000 genes with the highest remaining variance in both modalities, then compute Pearson correlation for every bulk against every sc library.
+- **k = 5** (about 10% of the 46 sc libraries; Ye used 10 for 133 libraries). Sensitivity runs used k = 0, 3, 8 and 10.
+- Ranks are counted per patient, because each patient's other timepoint is a legitimate near-tie.
+
+| k = 5 | result | chance |
+|---|---|---|
+| paired bulk's best sc patient is its own | 34 / 40 | about 4% |
+| paired sc's best bulk patient is its own | 24 / 40 | about 2% |
+| any bulk of an sc patient, best sc is the same patient | 41 / 55 | 3.9% |
+| AUC, same patient vs other patient (all bulk × sc) | 0.90 | 0.5 |
+| median r: paired / same patient, other timepoint / other patient | 0.17 / 0.10 / 0.00 | |
+| 99th percentile of r between different patients | 0.15 | |
+| own timepoint beats the same patient's other timepoint (bulk to sc) | 24 / 34 | about 50% |
+
+**How well can this check discriminate?** Moderately, and much less than in Ye 2026 (paired r 0.58 there). Whole blood against PBMC, and 3′ QuantSeq against 10x 5′, leave little shared donor signal.
+
+- A pass is good evidence that the bulk and sc come from the same patient.
+- A borderline or fail result is weaker evidence of a swap than in Ye.
+- The check cannot tell the two timepoints of one patient apart. Timepoint labels rest on GEO metadata alone.
+- The number of passes is stable across k (34, 33, 33 and 35 for k = 3, 5, 8, 10). Individual borderline rows move between borderline and pass.
+
+**Verdict rule.** Pass requires sex agreement, and the own patient must rank 1st in one direction and within the top 5 in the other.
+
+| pair | verdict (k = 5) | bulk batch | note |
+|---|---|---|---|
+| N087_AC | fail (own patient ranks 8 and 13) | 3 | The sc library's best bulk is N96_control_BC. N96 and N87 are both batch-3 samples with sex problems. This is a lead only. |
+| N158_BC | fail (ranks 11 and 18) | 5 | No strong alternative (best r 0.12). The same patient's AC pair passes. |
+| N032_BC | borderline (ranks 1 and 13) | 2 | |
+| N063_AC | borderline (ranks 3 and 14) | 2 | |
+| N106_AC | borderline (ranks 2 and 2) | 3 | |
+| N150_AC | borderline (ranks 1 and 8) | 5 | |
+| N159_AC | borderline (ranks 9 and 3) | 5 | |
+
+No pair was re-labelled.
+
+**N127 and N131.** The cell names `N127131ACV00` and `N1131ACV01` suggested that N127 and N131 might be one person. The expression data say they are not: N127V00 against either N131 library gives r ≈ 0. The two N131V01 libraries (Rd4a and Rd5) correlate at r = 0.70, so they are one person. The Rd5 N131 library's `orig.ident` ends in "AC" although its time is TOL. None of these libraries is paired.
+
+## Processing
+
+The run used the frozen ImMicro strict-QC code (bundle v5, copied unchanged and sha-checked), the same 20,097-gene GENCODE v49 axis and the same mapping rules.
+
+**Bulk**
+
+- One Salmon 1.10.0 gene × library table (GRCh38.p14, Ensembl 110) with 64,605 rows. Library names `itoxNNNNNN` join to GSMs through the GEO descriptions.
+- **Count type:** Salmon estimated read counts, stored as float64 exactly as deposited. Nothing was rounded. The deposited table has **0 fractional values** among 8.27 M entries, so the authors must have rounded before depositing. GEO calls them "raw counts".
+- 19,993 of 20,097 canonical genes are present; 104 are missing and marked unmeasured.
+- 3,462 source IDs are unknown to the reference, including 4 non-gene IDs (`ENSAP1-3`, `ENSP00000344568`). There are no duplicate targets.
+- Protocol: Lexogen QuantSeq 3′ FWD, 100 ng input, NextSeq 2000, 5 batches.
+
+**scRNA**
+
+- The source is a Seurat v4 object with 176,634 cells, 46 libraries and 36,601 features.
+- Only `RNA@counts` was exported (integer UMIs; `data` and `scale.data` were not). The export wrote one MatrixMarket file per library, from `code/export_seurat_counts.R`.
+- nCount_RNA, nFeature_RNA and percent.mt reproduce exactly from the exported counts.
+- The object carries symbols only. Ensembl IDs come from the CellRanger GRCh38-2020-A features.tsv (13 byte-identical GEO copies). `make.unique(gsub("_","-",symbol))` reproduces all 36,601 Seurat row names in order.
+- 19,227 canonical genes are present and 870 are missing (GENCODE v32 is older). **On the 6k panel, 5,759 of 6,000 genes are measured in sc, 5,992 in bulk and 5,752 in both.**
+- Library = sequencing round + PID_visit (one GEO GPEX GSM each).
+- **The object is already author-filtered.** The data show more than 200 genes, fewer than 5,000 genes and less than 5% mito per cell, but no UMI floor (minimum 368 UMIs).
+- `flag_conservative_review_pass` (at least 200 genes, at least 500 UMIs, at most 20% mito) was still applied. It removes 1,020 cells, all from N032's two libraries (940 from N032_AC, 80 from N032_BC). 154,698 of 155,718 author cells in the paired libraries are kept. The MAD flags are review-only columns.
+- `author_cell_type` is the authors' Azimuth `predicted.celltype.l2`. Level 1, level 3, the l2 score and the mapping score are extra columns appended after the Ye columns.
+- Chemistry: 10x 5′ GEX + V(D)J, CellRanger multi.
+
+## Files
+
+| file | contents |
+|---|---|
+| `features.npz` | One row per pair, in bulk GSM order. Ye keys, plus `timepoints`, `outcome` and pairing/metadata keys. `groups` = timepoint. `donor_ids` = patient. `bulk_raw` is 0 where not measured. |
+| `cells_panel6k.npz` | CSR int32 counts for the retained cells: 154,698 × 6,000, 57.0 M nonzero, compressed. |
+| `cells_full.npz` | The same cells on the full 20,097 axis, 170.0 M nonzero. Built by `tools/build_full_cells.py`, unmodified; see `cells_full.BUILD.json`. |
+| `cells_obs.parquet` | One row per retained cell, same order. The Ye columns come first, then author labels and outcome. |
+| `samples.csv`, `pairs.csv` | Row index, GEO fields, sex and expression checks, and the verdict for each pair. `pairs.csv` has sensitivity columns for k = 0, 3, 5, 8 and 10 (Ye has 10, 20 and 30). |
+| `identity_*.csv` | Full sex tables for all 128 bulks and 46 sc libraries, and the expression tables. |
+| `MANIFEST.json` | Sources with sha256, code with sha256, specimen evidence, discrimination by k, and all checks. |
+
+Checks passed:
+
+- Per row, the summed panel counts equal `pseudo_raw_sum[:, positions]` exactly, and the full-axis sums equal `pseudo_raw_sum`.
+- Cell counts equal `qc_cell_counts`, and nothing is stored outside the measured masks.
+- The `gene_positions` sha256 matches.
+- `prepare_dataset.py --dataset ji2025_chili` runs.