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Pseudodynamics+
Pseudodynamics+
  • About
  • API
    • Config
      • pseudodynamics._config.ExperimentConfig
    • Data Reader
      • pseudodynamics.reader.HigDim_AnnDS
      • pseudodynamics.reader.TwoTimpepoint_AnnDS
    • Models
      • pseudodynamics.models.MLP_models.MLP_surrogate
      • pseudodynamics.models.Spline_models.CubicSpline
      • pseudodynamics.models.Spline_models.MultiDim_CubicSpline
      • pseudodynamics.models._pde_informed_params.pde_params
      • pseudodynamics.models._pde_informed_params.log_pde_params
      • pseudodynamics.models._density_transport.Density_Transfer
    • Tools
      • pseudodynamics.functions.reader_funs.sample_deltax_from_knn
      • pseudodynamics.functions.reader_funs.compute_mellon_timesense_u
      • pseudodynamics.functions.reader_funs.train_test_split_adata
      • pseudodynamics.functions.reader_funs.make_coord_adata
      • pseudodynamics.functions.eval_funs.agg_param
      • pseudodynamics.functions.eval_funs.continuous_params
      • pseudodynamics.functions.eval_funs.density_shortterm_simulation
      • pseudodynamics.functions.eval_funs.project_params_to_pseudotime
      • pseudodynamics.functions.eval_funs.assign_nearest_cell
      • pseudodynamics.functions.eval_funs.W_distance
      • pseudodynamics.functions.eval_funs.KLD_density
    • Plotting
      • pseudodynamics.plotting_fns.param_plot.params_in_umap
      • pseudodynamics.plotting_fns.param_plot.plot_gene_trends
    • drift association test
      • pseudodynamics.de_test._base.fitGAM
      • pseudodynamics.de_test._association_test.AssociationTest
      • pseudodynamics.de_test._association_test.PseudotimeRestrictedAssociationTest
  • Tutorials
    • 1-1. Prepare Training Data
    • 1-2. Estimate single-cell density at observed time point. (Optional)
    • 2. Set up training config
    • 3. Evaluate behavior parameters
    • 4. Continuous Density Transport Analysis
  • References
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ConfigΒΆ

_config.ExperimentConfig([config, args, model])

Records and manages experiment configuration settings.
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pseudodynamics._config.ExperimentConfig
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