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README.md

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+---
+tags:
+- bulk-rna-seq
+- methylation
+- cancer
+- genomics
+pretty_name: TCGA PanCancer Atlas (trimmed, multi-omics)
+---
+
+# TCGA
+
+A trimmed multi-omics subset of the TCGA PanCancer Atlas (RNA + methylation + clinical), for use with [AUTOENCODIX](https://github.com/jan-forest/autoencodix_package) tutorials (`Ontix.ipynb`, `XModalix.ipynb`, `InputDataTutorials.ipynb`).
+
+## Contents
+
+- **3,246 samples** across 6 cancer types (fully paired RNA ∩ methylation ∩ clinical): BRCA (1,065), KIRC (509), THCA (497), SKCM (438), COAD (437), OV (300).
+- **7,941 genes** — full shared RNA ∩ methylation ∩ chromosome-ontology gene pool.
+- Files:
+  - `rna.parquet` — RNA expression, samples × genes
+  - `methylation.parquet` — methylation, samples × genes
+  - `clinical.parquet` — sample-level clinical/annotation metadata
+  - `chromosome_ont_lvl1_ncbi.txt`, `chromosome_ont_lvl2.txt` — chromosome-level ontology reference files (used by Ontix)
+
+## Loading
+
+```python
+from huggingface_hub import hf_hub_download
+import pandas as pd
+
+rna_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="rna.parquet")
+meth_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="methylation.parquet")
+clin_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="clinical.parquet")
+
+rna = pd.read_parquet(rna_path)
+```
+
+## License
+
+**Needs to be finalized.** This data derives from the TCGA PanCancer Atlas, governed by the NIH Genomic Data Sharing Policy rather than a standard copyright license (e.g. CC-BY) (?)