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ehrapy
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Contents:

  • Installation
  • API
    • ehrapy.io.read_csv
    • ehrapy.io.read_h5ad
    • ehrapy.io.read_fhir
    • ehrapy.io.write
    • ehrapy.data.mimic_2
    • ehrapy.data.mimic_2_preprocessed
    • ehrapy.data.mimic_3_demo
    • ehrapy.data.diabetes_130_raw
    • ehrapy.data.diabetes_130_fairlearn
    • ehrapy.data.heart_failure
    • ehrapy.data.chronic_kidney_disease
    • ehrapy.data.breast_tissue
    • ehrapy.data.cervical_cancer_risk_factors
    • ehrapy.data.dermatology
    • ehrapy.data.echocardiogram
    • ehrapy.data.heart_disease
    • ehrapy.data.hepatitis
    • ehrapy.data.statlog_heart
    • ehrapy.data.thyroid
    • ehrapy.data.breast_cancer_coimbra
    • ehrapy.data.parkinson_dataset_with_replicated_acoustic_features
    • ehrapy.data.parkinsons
    • ehrapy.data.parkinsons_disease_classification
    • ehrapy.data.parkinsons_telemonitoring
    • ehrapy.preprocessing.encode
    • ehrapy.preprocessing.pca
    • ehrapy.preprocessing.regress_out
    • ehrapy.preprocessing.subsample
    • ehrapy.preprocessing.balanced_sample
    • ehrapy.preprocessing.highly_variable_features
    • ehrapy.preprocessing.winsorize
    • ehrapy.preprocessing.clip_quantile
    • ehrapy.preprocessing.summarize_measurements
    • ehrapy.preprocessing.qc_metrics
    • ehrapy.preprocessing.qc_lab_measurements
    • ehrapy.preprocessing.mcar_test
    • ehrapy.preprocessing.detect_bias
    • ehrapy.preprocessing.explicit_impute
    • ehrapy.preprocessing.simple_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.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.annotate_text
    • ehrapy.tools.get_medcat_annotation_overview
    • ehrapy.tools.add_medcat_annotation_to_obs
    • 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.weibull_aft
    • ehrapy.tools.log_logistic_aft
    • ehrapy.tools.nelson_aalen
    • ehrapy.tools.weibull
    • ehrapy.tools.causal_inference
    • ehrapy.tools.CohortTracker
    • 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.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.causal_effect
    • ehrapy.anndata.infer_feature_types
    • ehrapy.anndata.feature_type_overview
    • ehrapy.anndata.replace_feature_types
    • ehrapy.anndata.df_to_anndata
    • ehrapy.anndata.anndata_to_df
    • ehrapy.anndata.move_to_obs
    • ehrapy.anndata.delete_from_obs
    • ehrapy.anndata.move_to_x
    • ehrapy.anndata.get_obs_df
    • ehrapy.anndata.get_var_df
    • ehrapy.anndata.get_rank_features_df
  • Tutorials
    • Introduction to ehrapy
    • MIMIC-II IAC Introduction
    • MIMIC-II IAC Patient Trajectory and Fate
    • MIMIC-II IAC Survival Analysis
    • MIMIC-II IAC Causal Inference
    • Extracting from free text with MedCAT
    • Using ehrapy with machine learning
    • Recommended literature
    • Ontology mapping
    • FHIR example
    • Cohort Tracking
    • Detection and dealing with bias in EHR data
    • Using ehrapy with Large Datasets
    • Patient Trajectory in COVID-19
  • Contributing guide
  • References
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Contributing guide
Copyright © 2025, Lukas Heumos, Philipp Ehmele, Eljas Roellin, Lilly May, Tim Treis, Altana Namsaraeva, Vladimir Shitov, Luke Zappia, Xinyue Zhang.
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