Feature/preclinical tables - #4
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July 23, 2026 13:02
…reatment responses
…ity and structure
- Created `inspect_CCLE_2015.R` and `inspect_ccle_2019.R` scripts to analyze CCLE datasets, including treatment responses and molecular profiles. - Updated `pixi.toml` to include `pymysql` dependency. - Enhanced database models in `tables.py` to include relationships for RNA-seq data, mutations, and copy number variations. - Modified `preclinical_seeding_coordinator.py` to create all necessary tables in the database.
… and gcsi extractions
- Implemented preclinical_seed_gcsi.py to handle GCSI dataset seeding, including cell lines, samples, treatment responses, and molecular data. - Implemented preclinical_seed_prism.py to handle PRISM dataset seeding, including cell lines, samples, and treatment responses. - Both scripts include data validation, cleaning functions, and support for auto-prefixing sample IDs. - Added command-line argument parsing for specifying data directories and dataset names.
…pabilities - Introduced support for loading RNA-seq, microarray, and copy number variation (CNV) datasets. - Added functions for transforming and cleaning molecular data values. - Implemented chunked processing for large CSV files to optimize memory usage. - Enhanced dataset metadata loading with validation checks for required fields. - Updated sample and treatment response seeding to accommodate new molecular data structures. - Created a new script for analyzing and summarizing copy number variation data from multiple sources. -Added seeding for drug and cell line data for database tables
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