tcga-bulk-data-preprocessing-with-omicverse

Automates TCGA data ingestion, metadata initialization, and survival analysis in omicverse.

• Load TCGA sample sheets, expression archives, and clinical carts.
• Initialize AnnData with raw/normalized counts and clinical metadata.
• Run survival analysis and export annotated AnnData files.
• Supports gene-level and all-gene survival analysis.

• Initializes AnnData with raw, FPKM, and TPM layers.
• Converts gene IDs to symbols and attaches patient info.
• Supports survival analysis with clinical date dependency.
• Exports annotated AnnData and survival summaries.
• Requires matching case IDs between sample sheet and archives.
• Spelling error in API: 'survial_init' (not 'survival_init').

1. 1.Verify presence of sample sheet, expression archive, and clinical cart.
2. 2.Instantiate pyTCGA helper and run adata_init() to build AnnData.
3. 3.Initialize metadata and survival attributes using adata_meta_init() and survival_init().
4. 4.Run survival analysis with survival_analysis() or survival_analysis_all().
5. 5.Save and reload AnnData files with write_h5ad() and adata_read().