--- a +++ b/docs/tutorials/index.md @@ -0,0 +1,57 @@ +--- +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](https://scverse.zulipchat.com/#narrow/channel/465075-ehrapy). +::: + +## Quick start + +```{eval-rst} +.. 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 + +```{eval-rst} +.. 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>`_. +``` + +[zulip forum]: https://scverse.zulipchat.com/#narrow/channel/465075-ehrapy