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General

  • Installation
  • API
    • Reading and writing
    • Preprocessing
      • ehrapy.preprocessing.encode
      • ehrapy.preprocessing.pca
      • ehrapy.preprocessing.regress_out
      • ehrapy.preprocessing.sample
      • ehrapy.preprocessing.highly_variable_features
      • ehrapy.preprocessing.winsorize
      • ehrapy.preprocessing.clip_quantile
      • ehrapy.preprocessing.summarize_measurements
      • ehrapy.preprocessing.filter_features
      • ehrapy.preprocessing.filter_observations
      • ehrapy.preprocessing.qc_metrics
      • ehrapy.preprocessing.qc_lab_measurements
      • ehrapy.preprocessing.mcar_test
      • ehrapy.preprocessing.detect_bias
      • ehrapy.preprocessing.missing_data_mask
      • ehrapy.preprocessing.explicit_impute
      • ehrapy.preprocessing.simple_impute
      • ehrapy.preprocessing.locf_impute
      • ehrapy.preprocessing.knn_impute
      • ehrapy.preprocessing.miss_forest_impute
      • ehrapy.preprocessing.mice_forest_impute
      • ehrapy.preprocessing.log_norm
      • ehrapy.preprocessing.maxabs_norm
      • ehrapy.preprocessing.minmax_norm
      • ehrapy.preprocessing.power_norm
      • ehrapy.preprocessing.quantile_norm
      • ehrapy.preprocessing.robust_scale_norm
      • ehrapy.preprocessing.scale_norm
      • ehrapy.preprocessing.offset_negative_values
      • ehrapy.preprocessing.combat
      • ehrapy.preprocessing.neighbors
      • ehrapy.preprocessing.variable_correlations
    • Tools
      • ehrapy.tools.tsne
      • ehrapy.tools.umap
      • ehrapy.tools.draw_graph
      • ehrapy.tools.diffmap
      • ehrapy.tools.embedding_density
      • ehrapy.tools.leiden
      • ehrapy.tools.dendrogram
      • ehrapy.tools.dpt
      • ehrapy.tools.paga
      • ehrapy.tools.rank_features_groups
      • ehrapy.tools.filter_rank_features_groups
      • ehrapy.tools.rank_features_supervised
      • ehrapy.tools.ingest
      • ehrapy.tools.ols
      • ehrapy.tools.glm
      • ehrapy.tools.kaplan_meier
      • ehrapy.tools.test_kmf_logrank
      • ehrapy.tools.test_nested_f_statistic
      • ehrapy.tools.cox_ph
      • ehrapy.tools.cox_ph_adjusted_curves
      • ehrapy.tools.weibull_aft
      • ehrapy.tools.log_logistic_aft
      • ehrapy.tools.nelson_aalen
      • ehrapy.tools.weibull
      • ehrapy.tools.causal_inference
      • ehrapy.tools.ncp
      • ehrapy.tools.CohortTracker
    • Plotting
      • ehrapy.plot.scatter
      • ehrapy.plot.heatmap
      • ehrapy.plot.dotplot
      • ehrapy.plot.tracksplot
      • ehrapy.plot.violin
      • ehrapy.plot.stacked_violin
      • ehrapy.plot.matrixplot
      • ehrapy.plot.clustermap
      • ehrapy.plot.ranking
      • ehrapy.plot.dendrogram
      • ehrapy.plot.catplot
      • ehrapy.plot.timeseries
      • ehrapy.plot.sankey_diagram
      • ehrapy.plot.sankey_diagram_time
      • ehrapy.plot.variable_correlations
      • ehrapy.plot.variable_dependencies
      • ehrapy.plot.missing_values_matrix
      • ehrapy.plot.missing_values_barplot
      • ehrapy.plot.missing_values_heatmap
      • ehrapy.plot.missing_values_dendrogram
      • ehrapy.plot.pca
      • ehrapy.plot.pca_loadings
      • ehrapy.plot.pca_variance_ratio
      • ehrapy.plot.pca_overview
      • ehrapy.plot.tsne
      • ehrapy.plot.umap
      • ehrapy.plot.diffmap
      • ehrapy.plot.draw_graph
      • ehrapy.plot.embedding
      • ehrapy.plot.embedding_density
      • ehrapy.plot.dpt_groups_pseudotime
      • ehrapy.plot.dpt_timeseries
      • ehrapy.plot.paga
      • ehrapy.plot.paga_path
      • ehrapy.plot.paga_compare
      • ehrapy.plot.rank_features_groups
      • ehrapy.plot.rank_features_groups_violin
      • ehrapy.plot.rank_features_groups_stacked_violin
      • ehrapy.plot.rank_features_groups_heatmap
      • ehrapy.plot.rank_features_groups_dotplot
      • ehrapy.plot.rank_features_groups_matrixplot
      • ehrapy.plot.rank_features_groups_tracksplot
      • ehrapy.plot.rank_features_supervised
      • ehrapy.plot.ols
      • ehrapy.plot.kaplan_meier
      • ehrapy.plot.cox_ph_forestplot
      • ehrapy.plot.cox_ph_adjusted_curves
      • ehrapy.plot.ncp
      • ehrapy.plot.ncp_cluster_trajectories
      • ehrapy.plot.causal_effect
    • Settings
      • ehrapy._settings.EhrapyConfig
  • Contributing guide
  • Changelog
  • References

Gallery

  • Tutorials
    • Introduction to ehrapy
    • MIMIC-II IAC Introduction
    • MIMIC-II IAC Patient Trajectory and Fate
    • MIMIC-II IAC Survival Analysis
    • MIMIC-II Treatment Effect Estimation with ehrapy
    • MIMIC-II IAC Causal Inference
    • Longitudinal Data Analysis
    • Ontology mapping
    • FHIR data
    • Cohort Tracking
    • Detection and mitigating bias in EHR data
    • Larger than memory datasets
    • Patient Trajectory in COVID-19

About

  • About ehrapy
  • Citing ehrapy
  • GitHub
  • .md

Tutorials

Contents

  • Quick start

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#

Introduction to ehrapy
MIMIC-II IAC Introduction
MIMIC-II IAC Patient Trajectory and Fate
MIMIC-II IAC Survival Analysis
MIMIC-II Treatment Effect Estimation with ehrapy
MIMIC-II IAC Causal Inference
Longitudinal Data Analysis
Ontology mapping
FHIR data
Cohort Tracking
Detection and mitigating bias in EHR data
Larger than memory datasets
Patient Trajectory in COVID-19

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References

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Introduction to ehrapy

Contents
  • Quick start

By Lukas Heumos, Philipp Ehmele, Eljas Roellin, Lilly May, Tim Treis, Altana Namsaraeva, Vladimir Shitov, Luke Zappia, Xinyue Zhang

© Copyright 2026, Lukas Heumos, Philipp Ehmele, Eljas Roellin, Lilly May, Tim Treis, Altana Namsaraeva, Vladimir Shitov, Luke Zappia, Xinyue Zhang..