| # Single-drug response data |
|
|
| This folder is a cleaned data layout for single-drug response prediction. |
| The bundled legacy collaborator reference package is located at this repository-relative path: |
|
|
| ```text |
| data/downstream/final_data/drug_response_pytorch/drug_response_pytorch |
| ``` |
|
|
| ## Runnable data path |
|
|
| From the repository root, use this directory as `--data_path` for `BioMod/drug_response/train.py`: |
|
|
| ```text |
| data/downstream/final_data/single_drug_response/data |
| ``` |
|
|
| Expected layout: |
|
|
| ```text |
| data/ |
| |-- GDSC/ |
| | |-- 1.Drug_listMon Jun 24 09_00_55 2019.csv |
| | `-- drug_graph_feat/*.hkl |
| `-- CCLE/ |
| |-- Cell_lines_annotations_20181226.txt |
| |-- GDSC_IC50.csv |
| `-- genomic_expression_561celllines_697genes_demap_features.csv |
| ``` |
|
|
| ## Previously recorded statistics |
|
|
| The figures below are retained from the existing dataset documentation; this path/comment audit did not recompute them. |
|
|
| - Drug information table: (266, 8) |
| - Drug graph files: 223 |
| - IC50 matrix: (266, 969) |
| - Cell-line expression matrix: (561, 697) |
| - Cell-line annotation table: (1461, 33) |
|
|
| ## Optional reference files |
|
|
| `optional_reference/` contains files from the original package that are not used by the current BioMod single-drug response script, including mutation, copy-number, methylation, threshold and DeepCDR reference outputs. Keep them for provenance or future multi-omics experiments. |
|
|
| ## Files |
|
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| See `MANIFEST.csv` for file sizes and checksums. See `SUMMARY.json` for machine-readable shape checks. |
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|
