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TRACERx Expression Data
VST-normalized gene expression data from the TRACERx lung cancer cohort.
Contents
tracerx_vst_counts.parquet: VST-normalized expression matrix (Parquet format)- Rows: 20136 genes
- Columns: 1051 samples
- Size: 106.0 MB
Usage
from huggingface_hub import hf_hub_download
import pandas as pd
# Download the expression data (Parquet - faster)
local_path = hf_hub_download(
repo_id="jruffle/tracerx_expression_data",
filename="tracerx_vst_counts.parquet",
repo_type="dataset"
)
# Load the data
expression_df = pd.read_parquet(local_path)
Data Format
- Index: Gene symbols (gene_id)
- Columns: Sample IDs
- Values: VST-normalized expression values
Why Parquet?
Parquet format provides:
- ~3x smaller file size than CSV
- ~10-100x faster loading times
- Native pandas support
License
This data is provided for research purposes as part of the CRUK Datathon 2025.
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