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General
Installation
API
Datasets
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.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
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.weibull_aft
ehrapy.tools.log_logistic_aft
ehrapy.tools.nelson_aalen
ehrapy.tools.weibull
ehrapy.tools.causal_inference
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.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
AnnData utilities
ehrapy.anndata.move_to_obs
ehrapy.anndata.move_to_x
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
Using ehrapy with machine learning
Ontology mapping
FHIR example
Cohort Tracking
Detection and dealing with bias in EHR data
Using ehrapy with Large Datasets
Patient Trajectory in COVID-19
About
About ehrapy
Citing ehrapy
GitHub
.md
.pdf
Datasets
Datasets
#
See
EHRData
’s
Datasets
for sample datasets available for ehrapy.
