TCGA bulk data preprocessing with omicverse

Overview

t_tcga.ipynb

ov.bulk.pyTCGA

Instructions

1. Gather required downloads
   • Confirm the user has:

     • gdc_sample_sheet.<date>.tsv

       from the TCGA Sample Sheet export.
     • The decompressed

       gdc_download_xxxxx

       directory containing expression archives.
     • The

       clinical.cart.<date>

       directory with clinical XML/JSON files.
   • Mention that sample data are available under

     omicverse_guide/docs/Tutorials-bulk/data/TCGA_OV/

     .
2. Initialise the TCGA helper
   • Import

     omicverse as ov

     (and

     scanpy as sc

     if plotting) then call

     ov.plot_set()

     .
   • Instantiate

     aml_tcga = ov.bulk.pyTCGA(sample_sheet_path, download_dir, clinical_dir)

     .
   • Run

     aml_tcga.adata_init()

     to build the AnnData object with raw counts, FPKM, and TPM layers.
3. Persist the dataset
   • Encourage saving the initial AnnData:

     aml_tcga.adata.write_h5ad('data/TCGA_OV/ov_tcga_raw.h5ad', compression='gzip')

     .
   • When reloading, reconstruct the class with the same paths and call

     aml_tcga.adata_read(<path>)

     .
4. Initialise metadata and clinical information
   • Populate sample metadata using

     aml_tcga.adata_meta_init()

     to convert gene IDs to symbols and attach patient info.
   • Add survival attributes via

     aml_tcga.survial_init()

     (note the intentional spelling in the API).
5. Perform survival analyses
   • Plot gene-level survival curves with

     aml_tcga.survival_analysis('GENE', layer='deseq_normalize', plot=True)

     .
   • To process all genes, call

     aml_tcga.survial_analysis_all()

     ; warn that it may take time.
6. Export results
   • Save enriched metadata to a new AnnData file (

     aml_tcga.adata.write_h5ad('.../ov_tcga_survial_all.h5ad', compression='gzip')

     ).
   • Suggest exporting summary tables (e.g., survival statistics) if users need to share outputs outside Python.
7. Troubleshooting tips
   • Ensure TCGA archives are fully extracted; missing XML/TSV files trigger parsing errors.
   • The helper expects matching case IDs between the sample sheet and expression files—direct users to re-download if IDs do not align.
   • Survival plots require clinical dates; if absent, instruct users to check the

     clinical_cart

     contents.

Examples

• "Read my TCGA OV download, initialise metadata, and plot MYC survival curves using DESeq-normalised counts."
• "Reload a saved AnnData file, attach survival annotations, and export the updated

  .h5ad

  ."
• "Run survival analysis for all genes and store the enriched dataset."

References

• Tutorial notebook:

  t_tcga.ipynb

• Sample dataset:

  data/TCGA_OV/

• Quick copy/paste commands:

  reference.md