cBioFormatter v0.3.0

This release adds a hands-on tutorial notebook to cbioformatter, making it easier for new users to get started with formatting clinical and genomic data for cBioPortal.

Installation

pip install --upgrade cbioformatter

or with uv:

uv add cbioformatter

Requires Python 3.10 or newer.

Highlights

Basic usage tutorial (examples/basic_usage.ipynb)

A new end-to-end Jupyter notebook walks researchers through the full cBioFormatter workflow: constructing a ClinicalStudy from pandas DataFrames, writing cBioPortal-compatible files, and running the offline validator. Bundled example data in examples/data/ means the notebook runs out of the box without any external files.

Quick start

import pandas as pd
from cbioformatter import ClinicalStudy

study = ClinicalStudy(
    study_id="my_study",
    name="My Study",
    description="A short description",
    cancer_type="brca",
    sample_data=sample_df,
    patient_data=patient_df,
)

study.write_files(output_dir="./studies")

See the README or examples/basic_usage.ipynb for a fuller walkthrough.

What's next

• See the open issues for the full backlog.

Full changelog

See CHANGELOG.md or the v0.2.0...v0.3.0 comparison for the complete list of changes.

Feedback

Please file an issue if you hit problems or have feature requests.