File size: 1,488 Bytes
faf1f6d 3830179 faf1f6d | 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 | # 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
See `MANIFEST.csv` for file sizes and checksums. See `SUMMARY.json` for machine-readable shape checks.
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