# Python for clinical programming


# Python projects for clinical programming

- [pycsr](https://pycsr.org/) - Python for Clinical Study Reports and Submission
- [csrlite](https://elong0527.github.io/csrlite/) - TLF generation for clinical study report
- [py4csr](https://github.com/yanmingyu92/py4csr) - Python for Clinical Study Reporting
- [pointblank](https://posit-dev.github.io/pointblank/) - SDTM and ADaM Validation
- [Synthetic CDISC Data Generator](https://github.com/yanmingyu92/synethetic_data)
- [CDISC Builder](https://github.com/hellomingchun/cdisc_builder) - Python package to build CDISC SDTM and ADaM datasets
- [CDISC SDTM & ADaM Builder](https://github.com/valofils/cdisc-sdtm-adam-builder)
- [yamaa](https://github.com/elong0527/yamaa) - YAML for CDISC mapping, derivation and data schema
- [ClinTrialDataFlow](https://github.com/ElvisCuiHan/ClinTrialDataFlow)
- [CDISC Rules Engine](https://github.com/cdisc-org/cdisc-rules-engine)
- [odmlib](https://github.com/swhume/odmlib) - Python package for working with CDISC ODM
- [cdisc-ct-downloader](https://github.com/A142763/cdisc-ct-downloader)
- [cdisc-library-client](https://github.com/cdisc-org/cdisc-library-client) - Python client for accessing the CDISC library
- [Forestly](https://github.com/elong0527/py-forestly)
- [pharmaverse Python](https://pharmaverse.org/e2eclinical/python/) - pharmaverse Python packages.


# Python ecosystem


## Data processing

- [polars](https://pola.rs)
- [pandas](https://pandas.pydata.org)


## Dataset comparison

- [datacompy](https://github.com/capitalone/datacompy)


## Data I/O

- [pyreadstat](https://github.com/Roche/pyreadstat)
- [pyarrow](https://arrow.apache.org/docs/python/)


## Dates & times

- [python-dateutil](https://dateutil.readthedocs.io)
- [pendulum](https://pendulum.eustace.io)
- [arrow](https://arrow.readthedocs.io)


## Statistics

- [numpy](https://numpy.org)
- [scipy](https://scipy.org)
- [statsmodels](https://www.statsmodels.org)
- [lifelines](https://github.com/CamDavidsonPilon/lifelines) - Survival analysis in Python
- [pingouin](https://pingouin-stats.org)
- [lifelines](https://lifelines.readthedocs.io)


## Plotting

- [matplotlib](https://matplotlib.org)
- [plotly](https://plotly.com/python/)
- [seaborn](https://seaborn.pydata.org)
- [altair](https://altair-viz.github.io)
- [plotnine](https://github.com/has2k1/plotnine)


## Tables & listings

- [great-tables](https://github.com/posit-dev/great-tables)
- [tableone](https://github.com/tompollard/tableone)
- [pysummaries](https://github.com/Genentech/pysummaries)
- [rtflite](https://github.com/pharmaverse/rtflite)


## Dashboards & interactive apps

- [Shiny for Python](https://shiny.posit.co/py/)
- [Streamlit](https://streamlit.io)
- [Marimo](https://marimo.io/)
- [Dash](https://dash.plotly.com)
- [Panel](https://panel.holoviz.org)


## Submission & packaging

- [pkglite](https://github.com/pharmaverse/py-pkglite)


## Toolchain

- [uv](https://docs.astral.sh/uv)
- [ruff](https://docs.astral.sh/ruff)
- [mypy](https://mypy-lang.org)
- [pytest](https://docs.pytest.org)
- [great-docs](https://posit-dev.github.io/great-docs/)


# Python package development

- [Python Packaging User Guide](https://packaging.python.org/en/latest)
- [pyOpenSci Python Package Guide](https://www.pyopensci.org/python-package-guide/index.html)
- [Python Packages](https://py-pkgs.org/)
- [Developing High-Quality Python Libraries](https://mcginniscommawill.com/guides/python-library-development/#table-of-contents)
- Publishing Python Packages: Test, share, and automate your projects


# PharmaSUG papers