| { |
| "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." |
| } |
