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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.iptw
ehrapy.tools.g_computation
ehrapy.tools.aipw
ehrapy.tools.propensity_score_matching
ehrapy.tools.t_learner
ehrapy.tools.s_learner
ehrapy.tools.x_learner
ehrapy.tools.covariate_balance
ehrapy.tools.positivity_check
ehrapy.tools.CausalEstimate
ehrapy.tools.ncp
ehrapy.tools.CohortTracker
ehrapy.tools.stratified_table_one
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.stratified_table_one
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.love_plot
ehrapy.plot.propensity_overlap
ehrapy.plot.causal_effect
Settings
ehrapy.settings
ehrapy.settings.override
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
Heterogeneous treatment effects on MIMIC-II
Causal inference on MIMIC-II
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
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