data/downstream/final_data/single_drug_response/README.md

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:

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:

data/downstream/final_data/single_drug_response/data

Expected layout:

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.