Datasets:
File size: 4,641 Bytes
13c45bc | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 | {
"n_genes": 13389,
"raw_feature_dim": 1109,
"pca_dim": 256,
"explained_variance_ratio_sum": 0.5395395755767822,
"channels": {
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"n_genes": 13389
},
"regulation": {
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"feature_dim": 86,
"tf_count_in_universe": 1191,
"dorothea_tfs": 367,
"trrust_tfs": 748,
"motif_count": 5876,
"motif_target_genes": 13132
},
"network_ontology": {
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"n_genes": 13389,
"feature_dim": 64,
"string_edge_count": 684790,
"reactome_group_count": 2450,
"complex_group_count": 1039
},
"expression": {
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"n_genes": 13389,
"feature_dim": 63,
"source_cells": {
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"gse131928_smartseq2_tpm": 7930,
"gse131928_10x_tpm": 16201,
"gse70630_oligodendroglioma_processed": 4347,
"gse89567_idh_processed": 6341,
"gse57872_gbm_processed_signed": 543,
"gse84465_gbm_counts": 3520
},
"sources": {
"gse174554_counts": {
"normalization": "raw_counts_to_cp10k_log1p",
"description": "GSE174554 matched primary/recurrent GBM raw counts",
"present_genes": 13106,
"compendium_manifest": "sources/gse174554_counts/manifest.json",
"approved_exclusions": [
{
"sample_name": "GSM5319529_SF8963",
"reason": "approved upstream corruption exclusion",
"evidence": {
"md5": "aaad42216f6818980171343e1cc57857",
"declared_nnz": 4855174,
"parseable_coordinate_lines": 4648192,
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}
}
]
},
"gse131928_smartseq2_tpm": {
"normalization": "tpm_to_log1p",
"description": "GSE131928 Smart-seq2",
"present_genes": 12825,
"compendium_manifest": "sources/gse131928_smartseq2_tpm/manifest.json",
"approved_exclusions": []
},
"gse131928_10x_tpm": {
"normalization": "tpm_to_log1p",
"description": "GSE131928 10x",
"present_genes": 12888,
"compendium_manifest": "sources/gse131928_10x_tpm/manifest.json",
"approved_exclusions": []
},
"gse70630_oligodendroglioma_processed": {
"normalization": "log_space_passthrough",
"description": "GSE70630 oligodendroglioma processed",
"present_genes": 12825,
"compendium_manifest": "sources/gse70630_oligodendroglioma_processed/manifest.json",
"approved_exclusions": []
},
"gse89567_idh_processed": {
"normalization": "log_space_passthrough",
"description": "GSE89567 IDH diffuse glioma processed",
"present_genes": 12825,
"compendium_manifest": "sources/gse89567_idh_processed/manifest.json",
"approved_exclusions": []
},
"gse57872_gbm_processed_signed": {
"normalization": "log_space_passthrough",
"description": "GSE57872 GBM processed signed",
"present_genes": 4874,
"compendium_manifest": "sources/gse57872_gbm_processed_signed/manifest.json",
"approved_exclusions": []
},
"gse84465_gbm_counts": {
"normalization": "raw_counts_to_cp10k_log1p",
"description": "GSE84465 GBM raw counts",
"present_genes": 12580,
"compendium_manifest": "sources/gse84465_gbm_counts/manifest.json",
"approved_exclusions": []
}
},
"compendium_manifest": "processed/stage_a/expression_compendium/compendium_manifest.json",
"input_policy": "loads only processed Stage A compendium artifacts; does not read raw GEO matrices directly",
"notes": {
"normalization_contract": "raw counts -> CP10K + log1p; TPM -> log1p; already log-space -> passthrough; Stage A compendium also stores global gene-wise z-score moments for training-time standardization",
"gse57872": "signed processed matrix is passthrough in the compendium; only descriptor statistics that require nonnegative support use per-gene minimum shift inside this H-GFB summary builder",
"approved_exclusion": []
}
}
},
"manifest_path": "data/processed/hgfb/hgfb_manifest.json"
} |