Archive 4 checkpoints (1-4)

paper-releases/20260928/diffusion/data/source_provenance/imperial_eskd/pairing/PAIRING_SUMMARY.json

@@ -0,0 +1,155 @@
+{
+  "sc_samples": 198,
+  "sc_patients": 63,
+  "sc_cells": 588389,
+  "sc_by_status": {
+    "positive": 149,
+    "negative": 38,
+    "recovery": 11
+  },
+  "bulk_columns": 336,
+  "bulk_patients": 105,
+  "bulk_by_status": {
+    "positive": 269,
+    "negative": 55,
+    "recovery": 12
+  },
+  "bulk_metadata_rows": 384,
+  "bulk_metadata_unique_ids": 367,
+  "bulk_metadata_ids_without_counts": [
+    "C113_positive_12",
+    "C113_positive_6",
+    "C116_positive_13",
+    "C116_positive_4",
+    "C116_positive_9",
+    "C134_negative",
+    "C137_positive_14",
+    "C138_positive_10",
+    "C138_positive_12",
+    "C141_positive_13",
+    "C141_positive_15",
+    "C147_positive_14",
+    "C169_positive_10",
+    "C170_positive_11",
+    "C170_positive_7",
+    "C170_positive_9",
+    "C187_positive_19",
+    "C196_negative",
+    "C20_positive_14",
+    "C23_positive_13",
+    "C29_negative",
+    "C49_positive_2",
+    "C49_positive_7",
+    "C57_positive_0",
+    "C58_positive_7",
+    "C60_positive_4",
+    "C60_positive_9",
+    "C70_negative",
+    "C73_positive_7",
+    "C82_positive_6",
+    "C87_positive_2"
+  ],
+  "bulk_metadata_duplicate_id_conflicts": {
+    "WHO_temp_severity": [
+      "C101_negative",
+      "C108_negative",
+      "C137_negative",
+      "C138_negative",
+      "C139_negative",
+      "C140_negative",
+      "C141_negative",
+      "C145_negative",
+      "C146_negative",
+      "C147_negative",
+      "C168_negative",
+      "C169_negative",
+      "C170_negative",
+      "C187_negative",
+      "C190_negative",
+      "C33_negative",
+      "C58_negative"
+    ],
+    "fatal_disease": [
+      "C101_negative",
+      "C108_negative",
+      "C137_negative",
+      "C138_negative",
+      "C139_negative",
+      "C140_negative",
+      "C141_negative",
+      "C145_negative",
+      "C146_negative",
+      "C147_negative",
+      "C168_negative",
+      "C169_negative",
+      "C170_negative",
+      "C187_negative",
+      "C190_negative",
+      "C33_negative",
+      "C58_negative"
+    ]
+  },
+  "bulk_day_label": {
+    "positive_columns": 269,
+    "label_equals_days_since_positive_swab": 132,
+    "label_equals_days_since_first_symptoms": 189,
+    "label_equals_max_of_both": 269
+  },
+  "patient_metadata_check": {
+    "sc_patients": 63,
+    "sc_patients_in_bulk_metadata": 63,
+    "sex_agree": 63,
+    "age_agree": 63,
+    "bulk_patients_with_varying_sex_or_age": 0
+  },
+  "author_filters_in_atlas": {
+    "exclude_nonzero_cells": 0,
+    "non_singlet_cells": 0,
+    "min_nCount_RNA_raw": 1005.0,
+    "min_nFeature_RNA_raw": 200.0,
+    "max_percentMito": 9.998711727976367
+  },
+  "primary_pairs": 172,
+  "primary_patients": 60,
+  "primary_by_status": {
+    "positive": 126,
+    "negative": 36,
+    "recovery": 10
+  },
+  "primary_by_basis": {
+    "patient+status+swab_day; symptom_day agrees": 110,
+    "patient+NEGATIVE; bulk metadata has no sample date (one NEGATIVE sample per patient on each side)": 36,
+    "patient+status+swab_day; neither side has a symptom-onset date": 26
+  },
+  "primary_patients_by_status": {
+    "negative": 36,
+    "positive": 38,
+    "recovery": 10
+  },
+  "sensitivity_candidates": 13,
+  "sensitivity_sc_samples": 10,
+  "sensitivity_offsets": {
+    "2.0": 13
+  },
+  "sc_without_exact_bulk": 26,
+  "sc_without_exact_bulk_reasons": {
+    "no bulk on the same swab day (nearest 2 d)": 10,
+    "no bulk on the same swab day (nearest 3 d)": 5,
+    "no bulk on the same swab day (nearest 7 d)": 3,
+    "no bulk column for this patient and status": 3,
+    "no bulk on the same swab day (nearest 5 d)": 2,
+    "no bulk on the same swab day (nearest 13 d)": 1,
+    "no bulk on the same swab day (nearest 12 d)": 1,
+    "no bulk on the same swab day (nearest 4 d)": 1
+  },
+  "bulk_without_sc": 164,
+  "coordinator_label_rule_reconciliation": {
+    "rule": "bulk column-name day == sc days_since_posswab (POSITIVE only)",
+    "exact_sc_samples": 76,
+    "exact_patients": 24,
+    "nearest_offset_1_day": 30,
+    "nearest_offset_2_days": 15,
+    "why_it_differs": "the column-name day counts from the earlier of symptom onset and positive swab, days_since_posswab counts from the swab; they differ whenever symptoms preceded the swab"
+  },
+  "rule": "POSITIVE and RECOVERY: same patient, same status, bulk time_from_first_positive_swab == sc days_since_posswab (same calendar day for that patient's swab date); where both sides carry a symptom-onset day it must agree too (it did for every match). NEGATIVE: same patient, NEGATIVE on both sides, one sample each; the bulk metadata has no NEGATIVE sample date, so these are patient+status pairs, not proven same draw. Every pair is 1:1."
+}

paper-releases/20260928/diffusion/data/source_provenance/imperial_eskd/reference_crosswalk/CROSSWALK.json

@@ -0,0 +1,198 @@
+{
+  "human_features": 33538,
+  "viral_features": 21,
+  "feature_types": [
+    "Gene Expression"
+  ],
+  "ordered_match_after_make_unique": true,
+  "positions_compared": 33538,
+  "make_unique_renamed_positions": [
+    {
+      "position": 2232,
+      "atlas_name": "RGS5.1",
+      "tenx_symbol": "RGS5",
+      "ensembl_id": "ENSG00000232995"
+    },
+    {
+      "position": 2999,
+      "atlas_name": "TBCE.1",
+      "tenx_symbol": "TBCE",
+      "ensembl_id": "ENSG00000284770"
+    },
+    {
+      "position": 4799,
+      "atlas_name": "PDE11A.1",
+      "tenx_symbol": "PDE11A",
+      "ensembl_id": "ENSG00000284741"
+    },
+    {
+      "position": 5438,
+      "atlas_name": "LINC01238.1",
+      "tenx_symbol": "LINC01238",
+      "ensembl_id": "ENSG00000261186"
+    },
+    {
+      "position": 5833,
+      "atlas_name": "PRSS50.1",
+      "tenx_symbol": "PRSS50",
+      "ensembl_id": "ENSG00000206549"
+    },
+    {
+      "position": 5953,
+      "atlas_name": "CYB561D2.1",
+      "tenx_symbol": "CYB561D2",
+      "ensembl_id": "ENSG00000271858"
+    },
+    {
+      "position": 6094,
+      "atlas_name": "ATXN7.1",
+      "tenx_symbol": "ATXN7",
+      "ensembl_id": "ENSG00000163635"
+    },
+    {
+      "position": 6462,
+      "atlas_name": "TXNRD3NB.1",
+      "tenx_symbol": "TXNRD3NB",
+      "ensembl_id": "ENSG00000206483"
+    },
+    {
+      "position": 6916,
+      "atlas_name": "CCDC39.1",
+      "tenx_symbol": "CCDC39",
+      "ensembl_id": "ENSG00000145075"
+    },
+    {
+      "position": 9597,
+      "atlas_name": "MATR3.1",
+      "tenx_symbol": "MATR3",
+      "ensembl_id": "ENSG00000015479"
+    },
+    {
+      "position": 11684,
+      "atlas_name": "SOD2.1",
+      "tenx_symbol": "SOD2",
+      "ensembl_id": "ENSG00000285441"
+    },
+    {
+      "position": 12722,
+      "atlas_name": "POLR2J3.1",
+      "tenx_symbol": "POLR2J3",
+      "ensembl_id": "ENSG00000285437"
+    },
+    {
+      "position": 13264,
+      "atlas_name": "ABCF2.1",
+      "tenx_symbol": "ABCF2",
+      "ensembl_id": "ENSG00000033050"
+    },
+    {
+      "position": 14008,
+      "atlas_name": "TMSB15B.1",
+      "tenx_symbol": "TMSB15B",
+      "ensembl_id": "ENSG00000269226"
+    },
+    {
+      "position": 14542,
+      "atlas_name": "PINX1.1",
+      "tenx_symbol": "PINX1",
+      "ensembl_id": "ENSG00000254093"
+    },
+    {
+      "position": 16459,
+      "atlas_name": "LINC01505.1",
+      "tenx_symbol": "LINC01505",
+      "ensembl_id": "ENSG00000234229"
+    },
+    {
+      "position": 17072,
+      "atlas_name": "IGF2.1",
+      "tenx_symbol": "IGF2",
+      "ensembl_id": "ENSG00000167244"
+    },
+    {
+      "position": 19043,
+      "atlas_name": "HSPA14.1",
+      "tenx_symbol": "HSPA14",
+      "ensembl_id": "ENSG00000187522"
+    },
+    {
+      "position": 20258,
+      "atlas_name": "EMG1.1",
+      "tenx_symbol": "EMG1",
+      "ensembl_id": "ENSG00000268439"
+    },
+    {
+      "position": 21711,
+      "atlas_name": "DIABLO.1",
+      "tenx_symbol": "DIABLO",
+      "ensembl_id": "ENSG00000184047"
+    },
+    {
+      "position": 23966,
+      "atlas_name": "LINC02203.1",
+      "tenx_symbol": "LINC02203",
+      "ensembl_id": "ENSG00000284988"
+    },
+    {
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+      "atlas_name": "COG8.1",
+      "tenx_symbol": "COG8",
+      "ensembl_id": "ENSG00000272617"
+    },
+    {
+      "position": 32974,
+      "atlas_name": "SCO2.1",
+      "tenx_symbol": "SCO2",
+      "ensembl_id": "ENSG00000284194"
+    },
+    {
+      "position": 33393,
+      "atlas_name": "H2BFS.1",
+      "tenx_symbol": "H2BFS",
+      "ensembl_id": "ENSG00000234289"
+    }
+  ],
+  "two_independent_copies_identical_id_symbol": true,
+  "viral_feature_names": [
+    "VIRAL-EBV1-(Human-gammaherpesvirus-4)",
+    "VIRAL-EBV2-(Human-herpesvirus-4)",
+    "VIRAL-ERVWE1-(syncytin).1",
+    "VIRAL-ERVWE1-(syncytin).2",
+    "VIRAL-ERVWE1-(syncytin).3",
+    "VIRAL-ERVWE1-(syncytin).4",
+    "VIRAL-ERVWE1-(syncytin).5",
+    "VIRAL-HERV-W.1",
+    "VIRAL-HERV-W.2",
+    "VIRAL-HERV-W.3",
+    "VIRAL-HERV-W.4",
+    "VIRAL-HHV-6A-(Human-Herpes-Virus-6)",
+    "VIRAL-HHV-6B-(Human-Herpes-Virus-6)",
+    "VIRAL-Herpes-Simplex-Virus-1-(Human-alphaherpesvirus-1)",
+    "VIRAL-Herpes-Simplex-Virus-2-(Human-alphaherpesvirus-1)",
+    "VIRAL-Measles-morbillivirus",
+    "VIRAL-Mumps-rubulavirus",
+    "VIRAL-Rubella",
+    "VIRAL-Varicella-Zoster-Virus-(VZV-Human-alphaherpesvirus-3)",
+    "VIRAL-Cytomegalovieus-(CMV)",
+    "VIRAL-SARS-CoV2"
+  ],
+  "files": [
+    {
+      "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/imperial_eskd_v1_20260928/reference_crosswalk/cellranger_GRCh38-3.0.0_features__from_GSE161529.tsv.gz",
+      "sha256": "d8b21cc094b58a3bdcd6c2b3cc7699399c4f14ff8f8611231a2c6da04791a354",
+      "bytes": 270380
+    },
+    {
+      "path": "/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/imperial_eskd_v1_20260928/reference_crosswalk/cellranger_GRCh38-3.0.0_features__from_GSM8012326.tsv.gz",
+      "sha256": "41314847b784a19147284b0f15d4e4ce9ee5ad4b0a277c300af1e477c4629ba4",
+      "bytes": 304728
+    }
+  ],
+  "copied_from": [
+    "/home/sj_server_1/gblee/rna_llm/datasets/raw/v6/geo_GSE161529/GSE161529_features.tsv.gz",
+    "/home/sj_server_1/gblee/rna_llm/datasets/raw/v6/geo_GSE253006/GSM8012326_TOF-023-W0_features.tsv.gz"
+  ],
+  "paper_statement": "Stephenson 2025 STAR Methods: 'We jointly aligned the ADT and gene expression libraries ... using CellRanger 4.0, using the reference 10X Genomics provided with the release of CellRanger 3.0'; viral reads were mapped separately (GENCODE v32 + 21 viral genomes, STARsolo)",
+  "rule": "Seurat make.unique(symbols) of the GRCh38-3.0.0 features.tsv equals the first 33,538 atlas var names position by position; IDs are assigned by position. The 21 trailing VIRAL- features have no human ID and map to nothing.",
+  "created_utc": "2026-09-28T02:52:31.315274+00:00"
+}