TCGA Bulk Data Preprocessing with OmicVerse

Overview

Use this skill for loading TCGA data from GDC downloads, building normalised expression matrices, attaching clinical metadata, and running survival analyses through ov.bulk.pyTCGA.

Instructions

1. Gather required downloads

Confirm the user has three items from the GDC Data Portal:

• gdc_sample_sheet.<date>.tsv — the sample sheet export
• Decompressed gdc_download_xxxxx/ directory with expression archives
• clinical.cart.<date>/ directory with clinical XML/JSON files

2. Initialise the TCGA helper

import omicverse as ov
import scanpy as sc
ov.plot_set()