omicverse.bulk.pyTCGA

omicverse.bulk.pyTCGA#

class omicverse.bulk.pyTCGA(gdc_sample_sheep, gdc_download_files, clinical_cart)[source]#

TCGA (The Cancer Genome Atlas) data analysis module.

This class provides comprehensive functionality for downloading, processing, and analyzing TCGA genomic and clinical data.

Parameters:

  • gdc_sample_sheep (str)

  • gdc_download_files (str)

  • clinical_cart (str)

__init__(gdc_sample_sheep, gdc_download_files, clinical_cart)[source]#

Initialize TCGA analysis module.

Parameters:

  • gdc_sample_sheep (str) – Path to TCGA Sample Sheet TSV file

  • gdc_download_files (str) – Path to downloaded TCGA data files directory

  • clinical_cart (str) – Path to TCGA clinical data tar.gz file

Methods

__init__(gdc_sample_sheep, ...)

Initialize TCGA analysis module.

adata_init()

adata_meta_init([var_names, obs_names])

Initialize AnnData metadata.

adata_read(path)

Read AnnData object from file.

expression_init()

Initialize expression matrices for TCGA data.

index_init()

Initialize gene indices for AnnData construction.

matrix_construct()

Construct AnnData object from expression matrices.

matrix_normalize(data)

Normalize expression matrix using DESeq2 method.

survial_analysis_all()

Perform survival analysis for all genes in the dataset.

survial_init()

Initialize survival analysis data.

survival_analysis(gene[, layer, plot, ...])

Perform survival analysis for a specific gene.
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