<jupyter_start><jupyter_text>Setup<jupyter_code>base="/srv/nas/mk2/projects/pan-cancer/TCGA_CCLE_GCP"
# read meta/data
tcga_meta = pd.read_csv(os.path.join(base, "TCGA/TCGA_GDC_ID_MAP.tsv"), sep="\t")
disease = tcga_meta[tcga_meta['Sample Type']=='Solid Tissue Normal']['Disease'].value_counts()
disease = list(disease[disease>=20].index)
disease
sample_type = ['Primary Tumor', 'Solid Tissue Normal']
params = {"device":"5",
          "n_features":2000,
          "steps":100,
          "embedding":2}
main(disease=disease, sample_type=sample_type, **params)<jupyter_output>Cuda is available: True
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