Datasets:
File size: 3,136 Bytes
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"source": "dense <Module>_largest_matrix.csv as received from the corresponding author",
"dense_shape": [
17350,
17350
],
"dense_values": [
"0.0",
"1.0"
],
"dense_line_ending": "CRLF",
"rebuild": "python disease_modelling/module_matrix_sparse.py to-matrix <M>_edges.csv out.csv <ref dense or gene_order.txt>",
"modules": {
"Asthma": {
"n_edges": 2366,
"n_nodes": 785,
"dense_md5": "b78d7fe5723d7d0baf02c71115e88190",
"dense_bytes": 1204328966,
"dense_gz": "modules/Asthma_largest_matrix.csv.gz",
"edges": "modules/Asthma_edges.csv"
},
"CAD": {
"n_edges": 1949,
"n_nodes": 751,
"dense_md5": "11704578713f3817b037bf504b28960b",
"dense_bytes": 1204328966,
"dense_gz": "modules/CAD_largest_matrix.csv.gz",
"edges": "modules/CAD_edges.csv"
},
"COPD": {
"n_edges": 806,
"n_nodes": 352,
"dense_md5": "f1ca0abf4fc8dc5ae43b0a3e1ef99aa3",
"dense_bytes": 1204328966,
"dense_gz": "modules/COPD_largest_matrix.csv.gz",
"edges": "modules/COPD_edges.csv"
},
"Fibrosis": {
"n_edges": 2366,
"n_nodes": 785,
"dense_md5": "b78d7fe5723d7d0baf02c71115e88190",
"dense_bytes": 1204328966,
"dense_gz": "modules/Fibrosis_largest_matrix.csv.gz",
"edges": "modules/Fibrosis_edges.csv"
},
"HI2023": {
"n_edges": 350950,
"n_nodes": 17350,
"dense_md5": "1d6140efdb58d8c383c799196cee07d1",
"dense_bytes": 1204328966,
"dense_gz": "modules/HI2023_largest_matrix.csv.gz",
"edges": "modules/HI2023_edges.csv"
},
"Inflammation": {
"n_edges": 1711,
"n_nodes": 523,
"dense_md5": "0452bc09ad328e49146762806d5a5f4f",
"dense_bytes": 1204328966,
"dense_gz": "modules/Inflammation_largest_matrix.csv.gz",
"edges": "modules/Inflammation_edges.csv"
},
"PAH": {
"n_edges": 741,
"n_nodes": 287,
"dense_md5": "cf0399f4331452865bd414ca3d3c0728",
"dense_bytes": 1204328966,
"dense_gz": "modules/PAH_largest_matrix.csv.gz",
"edges": "modules/PAH_edges.csv"
},
"Thrombosis": {
"n_edges": 566,
"n_nodes": 287,
"dense_md5": "0b5102922c61568b22ed53cb2a009324",
"dense_bytes": 1204328966,
"dense_gz": "modules/Thrombosis_largest_matrix.csv.gz",
"edges": "modules/Thrombosis_edges.csv"
}
},
"gene_order_file": "modules/gene_order.txt",
"gene_order_md5": "53580290d9f126208b043da1bdb11a3e",
"note": "Same content as disease_modelling/submission/data/modules/gene_lists/<M>.txt in the GitHub repo, which stores the pairs space-separated; COPD.txt carries a trailing '{}' edge-attribute column from nx.write_edgelist.",
"warning": "Fibrosis_largest_matrix.csv is byte-identical to Asthma_largest_matrix.csv (md5 b78d7fe5...), so one of the two is a copy of the wrong file. HI2023 is the whole interactome (350,950 edges), not a disease module.",
"use": "gunzip <M>_largest_matrix.csv.gz to get the exact file the analysis scripts read; the *_edges.csv are the same content as a sparse edge list."
} |