orphan: true

Tutorials

The easiest way to get familiar with ehrapy is to follow along with our tutorials.
Many are also designed to work seamlessly in Binder, a free cloud computing platform.

:::{note}
For questions about the usage of ehrapy use the zulip forum.
:::

Quick start

.. nbgallery::

   notebooks/ehrapy_introduction
   notebooks/mimic_2_introduction
   notebooks/mimic_2_fate
   notebooks/mimic_2_survival_analysis
   notebooks/mimic_2_effect_estimation
   notebooks/mimic_2_causal_inference
   notebooks/medcat
   notebooks/ml_usecases
   notebooks/ontology_mapping
   notebooks/fhir
   notebooks/cohort_tracking
   notebooks/bias
   notebooks/out_of_core
   notebooks/patient_trajectory

Glossary

.. tab-set::

    .. tab-item:: AnnData

        `AnnData <https://github.com/theislab/anndata>`_ is short for Annotated Data and is the primary datastructure that ehrapy uses.
        It is based on the principle of a single Numpy matrix X embraced by two Pandas DataFrames.
        All rows are called observations (in our case patients/patient visits or similar) and the columns
        are known as variables (any feature such as e.g. age, B12 level or similar).
        For a more in depth introduction please read the `AnnData paper <https://doi.org/10.1101/2021.12.16.473007>`_.


    .. tab-item:: scanpy

        The implementation of ehrapy is based on `scanpy <https://github.com/theislab/scanpy>`_, a framework to analyze single-cell sequencing data.
        ehrapy reuses the implemented algorithms in scanpy and wraps them for simple access.
        For a more in depth introduction please read the `Scanpy paper <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0>`_.