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moscot documentation
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  • Installation
  • User guide
  • User API
    • Biological Problems
      • moscot.problems.time.TemporalProblem
        • moscot.problems.time.TemporalProblem.add_problem
        • moscot.problems.time.TemporalProblem.annotation_mapping
        • moscot.problems.time.TemporalProblem.cell_transition
        • moscot.problems.time.TemporalProblem.compute_batch_distances
        • moscot.problems.time.TemporalProblem.compute_entropy
        • moscot.problems.time.TemporalProblem.compute_feature_correlation
        • moscot.problems.time.TemporalProblem.compute_interpolated_distance
        • moscot.problems.time.TemporalProblem.compute_random_distance
        • moscot.problems.time.TemporalProblem.compute_time_point_distances
        • moscot.problems.time.TemporalProblem.load
        • moscot.problems.time.TemporalProblem.prepare
        • moscot.problems.time.TemporalProblem.pull
        • moscot.problems.time.TemporalProblem.push
        • moscot.problems.time.TemporalProblem.remove_problem
        • moscot.problems.time.TemporalProblem.sankey
        • moscot.problems.time.TemporalProblem.save
        • moscot.problems.time.TemporalProblem.score_genes_for_marginals
        • moscot.problems.time.TemporalProblem.solve
        • moscot.problems.time.TemporalProblem.adata
        • moscot.problems.time.TemporalProblem.apoptosis_key
        • moscot.problems.time.TemporalProblem.cell_costs_source
        • moscot.problems.time.TemporalProblem.cell_costs_target
        • moscot.problems.time.TemporalProblem.posterior_growth_rates
        • moscot.problems.time.TemporalProblem.prior_growth_rates
        • moscot.problems.time.TemporalProblem.problem_kind
        • moscot.problems.time.TemporalProblem.problems
        • moscot.problems.time.TemporalProblem.proliferation_key
        • moscot.problems.time.TemporalProblem.solutions
        • moscot.problems.time.TemporalProblem.stage
        • moscot.problems.time.TemporalProblem.temporal_key
      • moscot.problems.time.LineageProblem
        • moscot.problems.time.LineageProblem.add_problem
        • moscot.problems.time.LineageProblem.annotation_mapping
        • moscot.problems.time.LineageProblem.cell_transition
        • moscot.problems.time.LineageProblem.compute_batch_distances
        • moscot.problems.time.LineageProblem.compute_entropy
        • moscot.problems.time.LineageProblem.compute_feature_correlation
        • moscot.problems.time.LineageProblem.compute_interpolated_distance
        • moscot.problems.time.LineageProblem.compute_random_distance
        • moscot.problems.time.LineageProblem.compute_time_point_distances
        • moscot.problems.time.LineageProblem.load
        • moscot.problems.time.LineageProblem.prepare
        • moscot.problems.time.LineageProblem.pull
        • moscot.problems.time.LineageProblem.push
        • moscot.problems.time.LineageProblem.remove_problem
        • moscot.problems.time.LineageProblem.sankey
        • moscot.problems.time.LineageProblem.save
        • moscot.problems.time.LineageProblem.score_genes_for_marginals
        • moscot.problems.time.LineageProblem.solve
        • moscot.problems.time.LineageProblem.adata
        • moscot.problems.time.LineageProblem.apoptosis_key
        • moscot.problems.time.LineageProblem.cell_costs_source
        • moscot.problems.time.LineageProblem.cell_costs_target
        • moscot.problems.time.LineageProblem.posterior_growth_rates
        • moscot.problems.time.LineageProblem.prior_growth_rates
        • moscot.problems.time.LineageProblem.problem_kind
        • moscot.problems.time.LineageProblem.problems
        • moscot.problems.time.LineageProblem.proliferation_key
        • moscot.problems.time.LineageProblem.solutions
        • moscot.problems.time.LineageProblem.stage
        • moscot.problems.time.LineageProblem.temporal_key
      • moscot.problems.space.AlignmentProblem
        • moscot.problems.space.AlignmentProblem.add_problem
        • moscot.problems.space.AlignmentProblem.align
        • moscot.problems.space.AlignmentProblem.annotation_mapping
        • moscot.problems.space.AlignmentProblem.cell_transition
        • moscot.problems.space.AlignmentProblem.compute_entropy
        • moscot.problems.space.AlignmentProblem.compute_feature_correlation
        • moscot.problems.space.AlignmentProblem.load
        • moscot.problems.space.AlignmentProblem.prepare
        • moscot.problems.space.AlignmentProblem.pull
        • moscot.problems.space.AlignmentProblem.push
        • moscot.problems.space.AlignmentProblem.remove_problem
        • moscot.problems.space.AlignmentProblem.save
        • moscot.problems.space.AlignmentProblem.solve
        • moscot.problems.space.AlignmentProblem.adata
        • moscot.problems.space.AlignmentProblem.batch_key
        • moscot.problems.space.AlignmentProblem.problem_kind
        • moscot.problems.space.AlignmentProblem.problems
        • moscot.problems.space.AlignmentProblem.solutions
        • moscot.problems.space.AlignmentProblem.spatial_key
        • moscot.problems.space.AlignmentProblem.stage
      • moscot.problems.space.MappingProblem
        • moscot.problems.space.MappingProblem.add_problem
        • moscot.problems.space.MappingProblem.annotation_mapping
        • moscot.problems.space.MappingProblem.cell_transition
        • moscot.problems.space.MappingProblem.compute_entropy
        • moscot.problems.space.MappingProblem.compute_feature_correlation
        • moscot.problems.space.MappingProblem.correlate
        • moscot.problems.space.MappingProblem.impute
        • moscot.problems.space.MappingProblem.load
        • moscot.problems.space.MappingProblem.prepare
        • moscot.problems.space.MappingProblem.pull
        • moscot.problems.space.MappingProblem.push
        • moscot.problems.space.MappingProblem.remove_problem
        • moscot.problems.space.MappingProblem.save
        • moscot.problems.space.MappingProblem.solve
        • moscot.problems.space.MappingProblem.spatial_correspondence
        • moscot.problems.space.MappingProblem.adata
        • moscot.problems.space.MappingProblem.adata_sc
        • moscot.problems.space.MappingProblem.adata_sp
        • moscot.problems.space.MappingProblem.batch_key
        • moscot.problems.space.MappingProblem.filtered_vars
        • moscot.problems.space.MappingProblem.problem_kind
        • moscot.problems.space.MappingProblem.problems
        • moscot.problems.space.MappingProblem.solutions
        • moscot.problems.space.MappingProblem.spatial_key
        • moscot.problems.space.MappingProblem.stage
      • moscot.problems.spatiotemporal.SpatioTemporalProblem
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.add_problem
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.align
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.annotation_mapping
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.cell_transition
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.compute_batch_distances
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.compute_entropy
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.compute_feature_correlation
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.compute_interpolated_distance
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.compute_random_distance
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.compute_time_point_distances
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.load
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.prepare
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.pull
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.push
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.remove_problem
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.sankey
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.save
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.score_genes_for_marginals
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.solve
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.adata
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.apoptosis_key
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.batch_key
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.cell_costs_source
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.cell_costs_target
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.posterior_growth_rates
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.prior_growth_rates
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.problem_kind
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.problems
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.proliferation_key
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.solutions
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.spatial_key
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.stage
        • moscot.problems.spatiotemporal.SpatioTemporalProblem.temporal_key
      • moscot.problems.cross_modality.TranslationProblem
        • moscot.problems.cross_modality.TranslationProblem.add_problem
        • moscot.problems.cross_modality.TranslationProblem.annotation_mapping
        • moscot.problems.cross_modality.TranslationProblem.cell_transition
        • moscot.problems.cross_modality.TranslationProblem.compute_entropy
        • moscot.problems.cross_modality.TranslationProblem.compute_feature_correlation
        • moscot.problems.cross_modality.TranslationProblem.load
        • moscot.problems.cross_modality.TranslationProblem.prepare
        • moscot.problems.cross_modality.TranslationProblem.pull
        • moscot.problems.cross_modality.TranslationProblem.push
        • moscot.problems.cross_modality.TranslationProblem.remove_problem
        • moscot.problems.cross_modality.TranslationProblem.save
        • moscot.problems.cross_modality.TranslationProblem.solve
        • moscot.problems.cross_modality.TranslationProblem.translate
        • moscot.problems.cross_modality.TranslationProblem.adata
        • moscot.problems.cross_modality.TranslationProblem.adata_src
        • moscot.problems.cross_modality.TranslationProblem.adata_tgt
        • moscot.problems.cross_modality.TranslationProblem.batch_key
        • moscot.problems.cross_modality.TranslationProblem.problem_kind
        • moscot.problems.cross_modality.TranslationProblem.problems
        • moscot.problems.cross_modality.TranslationProblem.solutions
        • moscot.problems.cross_modality.TranslationProblem.stage
    • Generic Problems
      • moscot.problems.generic.SinkhornProblem
        • moscot.problems.generic.SinkhornProblem.add_problem
        • moscot.problems.generic.SinkhornProblem.cell_transition
        • moscot.problems.generic.SinkhornProblem.compute_entropy
        • moscot.problems.generic.SinkhornProblem.compute_feature_correlation
        • moscot.problems.generic.SinkhornProblem.load
        • moscot.problems.generic.SinkhornProblem.prepare
        • moscot.problems.generic.SinkhornProblem.pull
        • moscot.problems.generic.SinkhornProblem.push
        • moscot.problems.generic.SinkhornProblem.remove_problem
        • moscot.problems.generic.SinkhornProblem.save
        • moscot.problems.generic.SinkhornProblem.solve
        • moscot.problems.generic.SinkhornProblem.adata
        • moscot.problems.generic.SinkhornProblem.batch_key
        • moscot.problems.generic.SinkhornProblem.problem_kind
        • moscot.problems.generic.SinkhornProblem.problems
        • moscot.problems.generic.SinkhornProblem.solutions
        • moscot.problems.generic.SinkhornProblem.stage
      • moscot.problems.generic.GWProblem
        • moscot.problems.generic.GWProblem.add_problem
        • moscot.problems.generic.GWProblem.cell_transition
        • moscot.problems.generic.GWProblem.compute_entropy
        • moscot.problems.generic.GWProblem.compute_feature_correlation
        • moscot.problems.generic.GWProblem.load
        • moscot.problems.generic.GWProblem.prepare
        • moscot.problems.generic.GWProblem.pull
        • moscot.problems.generic.GWProblem.push
        • moscot.problems.generic.GWProblem.remove_problem
        • moscot.problems.generic.GWProblem.save
        • moscot.problems.generic.GWProblem.solve
        • moscot.problems.generic.GWProblem.adata
        • moscot.problems.generic.GWProblem.batch_key
        • moscot.problems.generic.GWProblem.problem_kind
        • moscot.problems.generic.GWProblem.problems
        • moscot.problems.generic.GWProblem.solutions
        • moscot.problems.generic.GWProblem.stage
      • moscot.problems.generic.FGWProblem
        • moscot.problems.generic.FGWProblem.add_problem
        • moscot.problems.generic.FGWProblem.cell_transition
        • moscot.problems.generic.FGWProblem.compute_entropy
        • moscot.problems.generic.FGWProblem.compute_feature_correlation
        • moscot.problems.generic.FGWProblem.load
        • moscot.problems.generic.FGWProblem.prepare
        • moscot.problems.generic.FGWProblem.pull
        • moscot.problems.generic.FGWProblem.push
        • moscot.problems.generic.FGWProblem.remove_problem
        • moscot.problems.generic.FGWProblem.save
        • moscot.problems.generic.FGWProblem.solve
        • moscot.problems.generic.FGWProblem.adata
        • moscot.problems.generic.FGWProblem.batch_key
        • moscot.problems.generic.FGWProblem.problem_kind
        • moscot.problems.generic.FGWProblem.problems
        • moscot.problems.generic.FGWProblem.solutions
        • moscot.problems.generic.FGWProblem.stage
    • Plotting
      • moscot.plotting.cell_transition
      • moscot.plotting.sankey
      • moscot.plotting.push
      • moscot.plotting.pull
    • Datasets
      • moscot.datasets.bone_marrow
      • moscot.datasets.c_elegans
      • moscot.datasets.drosophila
      • moscot.datasets.hspc
      • moscot.datasets.mosta
      • moscot.datasets.pancreas_multiome
      • moscot.datasets.sciplex
      • moscot.datasets.sim_align
      • moscot.datasets.simulate_data
      • moscot.datasets.tedsim
      • moscot.datasets.zebrafish
  • Developer API
    • Backends
      • moscot.backends.ott.SinkhornSolver
        • moscot.backends.ott.SinkhornSolver.__call__
        • moscot.backends.ott.SinkhornSolver.is_low_rank
        • moscot.backends.ott.SinkhornSolver.problem_kind
        • moscot.backends.ott.SinkhornSolver.rank
        • moscot.backends.ott.SinkhornSolver.solver
        • moscot.backends.ott.SinkhornSolver.xy
      • moscot.backends.ott.GWSolver
        • moscot.backends.ott.GWSolver.__call__
        • moscot.backends.ott.GWSolver.is_fused
        • moscot.backends.ott.GWSolver.is_low_rank
        • moscot.backends.ott.GWSolver.problem_kind
        • moscot.backends.ott.GWSolver.rank
        • moscot.backends.ott.GWSolver.solver
        • moscot.backends.ott.GWSolver.x
        • moscot.backends.ott.GWSolver.xy
        • moscot.backends.ott.GWSolver.y
      • moscot.backends.ott.OTTOutput
        • moscot.backends.ott.OTTOutput.as_linear_operator
        • moscot.backends.ott.OTTOutput.chain
        • moscot.backends.ott.OTTOutput.plot_costs
        • moscot.backends.ott.OTTOutput.plot_errors
        • moscot.backends.ott.OTTOutput.pull
        • moscot.backends.ott.OTTOutput.push
        • moscot.backends.ott.OTTOutput.sparsify
        • moscot.backends.ott.OTTOutput.to
        • moscot.backends.ott.OTTOutput.a
        • moscot.backends.ott.OTTOutput.b
        • moscot.backends.ott.OTTOutput.converged
        • moscot.backends.ott.OTTOutput.cost
        • moscot.backends.ott.OTTOutput.dtype
        • moscot.backends.ott.OTTOutput.is_linear
        • moscot.backends.ott.OTTOutput.is_low_rank
        • moscot.backends.ott.OTTOutput.potentials
        • moscot.backends.ott.OTTOutput.rank
        • moscot.backends.ott.OTTOutput.shape
        • moscot.backends.ott.OTTOutput.transport_matrix
      • moscot.backends.ott.GraphOTTOutput
        • moscot.backends.ott.GraphOTTOutput.as_linear_operator
        • moscot.backends.ott.GraphOTTOutput.chain
        • moscot.backends.ott.GraphOTTOutput.plot_costs
        • moscot.backends.ott.GraphOTTOutput.plot_errors
        • moscot.backends.ott.GraphOTTOutput.pull
        • moscot.backends.ott.GraphOTTOutput.push
        • moscot.backends.ott.GraphOTTOutput.sparsify
        • moscot.backends.ott.GraphOTTOutput.to
        • moscot.backends.ott.GraphOTTOutput.a
        • moscot.backends.ott.GraphOTTOutput.b
        • moscot.backends.ott.GraphOTTOutput.converged
        • moscot.backends.ott.GraphOTTOutput.cost
        • moscot.backends.ott.GraphOTTOutput.dtype
        • moscot.backends.ott.GraphOTTOutput.is_linear
        • moscot.backends.ott.GraphOTTOutput.is_low_rank
        • moscot.backends.ott.GraphOTTOutput.potentials
        • moscot.backends.ott.GraphOTTOutput.rank
        • moscot.backends.ott.GraphOTTOutput.shape
        • moscot.backends.ott.GraphOTTOutput.transport_matrix
      • moscot.backends.utils.get_solver
      • moscot.backends.utils.get_available_backends
    • Costs
      • moscot.costs.BarcodeDistance
        • moscot.costs.BarcodeDistance.__call__
        • moscot.costs.BarcodeDistance.adata
        • moscot.costs.BarcodeDistance.barcodes
      • moscot.costs.LeafDistance
        • moscot.costs.LeafDistance.__call__
        • moscot.costs.LeafDistance.adata
        • moscot.costs.LeafDistance.tree
      • moscot.costs.get_cost
      • moscot.costs.get_available_costs
      • moscot.costs.register_cost
    • Base
      • moscot.base.problems.BaseProblem
        • moscot.base.problems.BaseProblem.load
        • moscot.base.problems.BaseProblem.prepare
        • moscot.base.problems.BaseProblem.save
        • moscot.base.problems.BaseProblem.solve
        • moscot.base.problems.BaseProblem.problem_kind
        • moscot.base.problems.BaseProblem.stage
      • moscot.base.problems.OTProblem
        • moscot.base.problems.OTProblem.estimate_marginals
        • moscot.base.problems.OTProblem.load
        • moscot.base.problems.OTProblem.prepare
        • moscot.base.problems.OTProblem.pull
        • moscot.base.problems.OTProblem.push
        • moscot.base.problems.OTProblem.save
        • moscot.base.problems.OTProblem.set_graph_x
        • moscot.base.problems.OTProblem.set_graph_xy
        • moscot.base.problems.OTProblem.set_graph_y
        • moscot.base.problems.OTProblem.set_solution
        • moscot.base.problems.OTProblem.set_x
        • moscot.base.problems.OTProblem.set_xy
        • moscot.base.problems.OTProblem.set_y
        • moscot.base.problems.OTProblem.solve
        • moscot.base.problems.OTProblem.a
        • moscot.base.problems.OTProblem.adata_src
        • moscot.base.problems.OTProblem.adata_tgt
        • moscot.base.problems.OTProblem.b
        • moscot.base.problems.OTProblem.problem_kind
        • moscot.base.problems.OTProblem.shape
        • moscot.base.problems.OTProblem.solution
        • moscot.base.problems.OTProblem.solver
        • moscot.base.problems.OTProblem.stage
        • moscot.base.problems.OTProblem.x
        • moscot.base.problems.OTProblem.xy
        • moscot.base.problems.OTProblem.y
      • moscot.base.problems.BirthDeathProblem
        • moscot.base.problems.BirthDeathProblem.estimate_marginals
        • moscot.base.problems.BirthDeathProblem.load
        • moscot.base.problems.BirthDeathProblem.prepare
        • moscot.base.problems.BirthDeathProblem.pull
        • moscot.base.problems.BirthDeathProblem.push
        • moscot.base.problems.BirthDeathProblem.save
        • moscot.base.problems.BirthDeathProblem.score_genes_for_marginals
        • moscot.base.problems.BirthDeathProblem.set_graph_x
        • moscot.base.problems.BirthDeathProblem.set_graph_xy
        • moscot.base.problems.BirthDeathProblem.set_graph_y
        • moscot.base.problems.BirthDeathProblem.set_solution
        • moscot.base.problems.BirthDeathProblem.set_x
        • moscot.base.problems.BirthDeathProblem.set_xy
        • moscot.base.problems.BirthDeathProblem.set_y
        • moscot.base.problems.BirthDeathProblem.solve
        • moscot.base.problems.BirthDeathProblem.a
        • moscot.base.problems.BirthDeathProblem.adata
        • moscot.base.problems.BirthDeathProblem.adata_src
        • moscot.base.problems.BirthDeathProblem.adata_tgt
        • moscot.base.problems.BirthDeathProblem.apoptosis_key
        • moscot.base.problems.BirthDeathProblem.b
        • moscot.base.problems.BirthDeathProblem.delta
        • moscot.base.problems.BirthDeathProblem.posterior_growth_rates
        • moscot.base.problems.BirthDeathProblem.prior_growth_rates
        • moscot.base.problems.BirthDeathProblem.problem_kind
        • moscot.base.problems.BirthDeathProblem.proliferation_key
        • moscot.base.problems.BirthDeathProblem.shape
        • moscot.base.problems.BirthDeathProblem.solution
        • moscot.base.problems.BirthDeathProblem.solver
        • moscot.base.problems.BirthDeathProblem.stage
        • moscot.base.problems.BirthDeathProblem.x
        • moscot.base.problems.BirthDeathProblem.xy
        • moscot.base.problems.BirthDeathProblem.y
      • moscot.base.problems.BaseCompoundProblem
        • moscot.base.problems.BaseCompoundProblem.add_problem
        • moscot.base.problems.BaseCompoundProblem.load
        • moscot.base.problems.BaseCompoundProblem.prepare
        • moscot.base.problems.BaseCompoundProblem.pull
        • moscot.base.problems.BaseCompoundProblem.push
        • moscot.base.problems.BaseCompoundProblem.remove_problem
        • moscot.base.problems.BaseCompoundProblem.save
        • moscot.base.problems.BaseCompoundProblem.solve
        • moscot.base.problems.BaseCompoundProblem.adata
        • moscot.base.problems.BaseCompoundProblem.problem_kind
        • moscot.base.problems.BaseCompoundProblem.problems
        • moscot.base.problems.BaseCompoundProblem.solutions
        • moscot.base.problems.BaseCompoundProblem.stage
      • moscot.base.problems.CompoundProblem
        • moscot.base.problems.CompoundProblem.add_problem
        • moscot.base.problems.CompoundProblem.load
        • moscot.base.problems.CompoundProblem.prepare
        • moscot.base.problems.CompoundProblem.pull
        • moscot.base.problems.CompoundProblem.push
        • moscot.base.problems.CompoundProblem.remove_problem
        • moscot.base.problems.CompoundProblem.save
        • moscot.base.problems.CompoundProblem.solve
        • moscot.base.problems.CompoundProblem.adata
        • moscot.base.problems.CompoundProblem.problem_kind
        • moscot.base.problems.CompoundProblem.problems
        • moscot.base.problems.CompoundProblem.solutions
        • moscot.base.problems.CompoundProblem.stage
      • moscot.base.cost.BaseCost
        • moscot.base.cost.BaseCost.__call__
        • moscot.base.cost.BaseCost.adata
      • moscot.base.problems.AnalysisMixin
        • moscot.base.problems.AnalysisMixin.compute_entropy
        • moscot.base.problems.AnalysisMixin.compute_feature_correlation
        • moscot.base.problems.AnalysisMixin.pull
        • moscot.base.problems.AnalysisMixin.push
        • moscot.base.problems.AnalysisMixin.adata
        • moscot.base.problems.AnalysisMixin.problems
        • moscot.base.problems.AnalysisMixin.solutions
      • moscot.base.problems.BirthDeathMixin
        • moscot.base.problems.BirthDeathMixin.score_genes_for_marginals
        • moscot.base.problems.BirthDeathMixin.adata
        • moscot.base.problems.BirthDeathMixin.apoptosis_key
        • moscot.base.problems.BirthDeathMixin.proliferation_key
      • moscot.base.problems.birth_death.beta
      • moscot.base.problems.birth_death.delta
      • moscot.base.solver.BaseSolver
        • moscot.base.solver.BaseSolver.__call__
        • moscot.base.solver.BaseSolver.problem_kind
      • moscot.base.solver.OTSolver
        • moscot.base.solver.OTSolver.__call__
        • moscot.base.solver.OTSolver.problem_kind
      • moscot.base.output.BaseDiscreteSolverOutput
        • moscot.base.output.BaseDiscreteSolverOutput.as_linear_operator
        • moscot.base.output.BaseDiscreteSolverOutput.chain
        • moscot.base.output.BaseDiscreteSolverOutput.pull
        • moscot.base.output.BaseDiscreteSolverOutput.push
        • moscot.base.output.BaseDiscreteSolverOutput.sparsify
        • moscot.base.output.BaseDiscreteSolverOutput.to
        • moscot.base.output.BaseDiscreteSolverOutput.a
        • moscot.base.output.BaseDiscreteSolverOutput.b
        • moscot.base.output.BaseDiscreteSolverOutput.converged
        • moscot.base.output.BaseDiscreteSolverOutput.cost
        • moscot.base.output.BaseDiscreteSolverOutput.dtype
        • moscot.base.output.BaseDiscreteSolverOutput.is_linear
        • moscot.base.output.BaseDiscreteSolverOutput.is_low_rank
        • moscot.base.output.BaseDiscreteSolverOutput.potentials
        • moscot.base.output.BaseDiscreteSolverOutput.rank
        • moscot.base.output.BaseDiscreteSolverOutput.shape
        • moscot.base.output.BaseDiscreteSolverOutput.transport_matrix
      • moscot.base.output.MatrixSolverOutput
        • moscot.base.output.MatrixSolverOutput.as_linear_operator
        • moscot.base.output.MatrixSolverOutput.chain
        • moscot.base.output.MatrixSolverOutput.pull
        • moscot.base.output.MatrixSolverOutput.push
        • moscot.base.output.MatrixSolverOutput.sparsify
        • moscot.base.output.MatrixSolverOutput.to
        • moscot.base.output.MatrixSolverOutput.a
        • moscot.base.output.MatrixSolverOutput.b
        • moscot.base.output.MatrixSolverOutput.converged
        • moscot.base.output.MatrixSolverOutput.cost
        • moscot.base.output.MatrixSolverOutput.dtype
        • moscot.base.output.MatrixSolverOutput.is_linear
        • moscot.base.output.MatrixSolverOutput.is_low_rank
        • moscot.base.output.MatrixSolverOutput.potentials
        • moscot.base.output.MatrixSolverOutput.rank
        • moscot.base.output.MatrixSolverOutput.shape
        • moscot.base.output.MatrixSolverOutput.transport_matrix
      • moscot.base.solver.BaseSolver
        • moscot.base.solver.BaseSolver.__call__
        • moscot.base.solver.BaseSolver.problem_kind
      • moscot.base.solver.OTSolver
        • moscot.base.solver.OTSolver.__call__
        • moscot.base.solver.OTSolver.problem_kind
      • moscot.base.output.BaseDiscreteSolverOutput
        • moscot.base.output.BaseDiscreteSolverOutput.as_linear_operator
        • moscot.base.output.BaseDiscreteSolverOutput.chain
        • moscot.base.output.BaseDiscreteSolverOutput.pull
        • moscot.base.output.BaseDiscreteSolverOutput.push
        • moscot.base.output.BaseDiscreteSolverOutput.sparsify
        • moscot.base.output.BaseDiscreteSolverOutput.to
        • moscot.base.output.BaseDiscreteSolverOutput.a
        • moscot.base.output.BaseDiscreteSolverOutput.b
        • moscot.base.output.BaseDiscreteSolverOutput.converged
        • moscot.base.output.BaseDiscreteSolverOutput.cost
        • moscot.base.output.BaseDiscreteSolverOutput.dtype
        • moscot.base.output.BaseDiscreteSolverOutput.is_linear
        • moscot.base.output.BaseDiscreteSolverOutput.is_low_rank
        • moscot.base.output.BaseDiscreteSolverOutput.potentials
        • moscot.base.output.BaseDiscreteSolverOutput.rank
        • moscot.base.output.BaseDiscreteSolverOutput.shape
        • moscot.base.output.BaseDiscreteSolverOutput.transport_matrix
      • moscot.base.output.MatrixSolverOutput
        • moscot.base.output.MatrixSolverOutput.as_linear_operator
        • moscot.base.output.MatrixSolverOutput.chain
        • moscot.base.output.MatrixSolverOutput.pull
        • moscot.base.output.MatrixSolverOutput.push
        • moscot.base.output.MatrixSolverOutput.sparsify
        • moscot.base.output.MatrixSolverOutput.to
        • moscot.base.output.MatrixSolverOutput.a
        • moscot.base.output.MatrixSolverOutput.b
        • moscot.base.output.MatrixSolverOutput.converged
        • moscot.base.output.MatrixSolverOutput.cost
        • moscot.base.output.MatrixSolverOutput.dtype
        • moscot.base.output.MatrixSolverOutput.is_linear
        • moscot.base.output.MatrixSolverOutput.is_low_rank
        • moscot.base.output.MatrixSolverOutput.potentials
        • moscot.base.output.MatrixSolverOutput.rank
        • moscot.base.output.MatrixSolverOutput.shape
        • moscot.base.output.MatrixSolverOutput.transport_matrix
    • Utils
      • moscot.utils.subset_policy.SubsetPolicy
        • moscot.utils.subset_policy.SubsetPolicy.add_node
        • moscot.utils.subset_policy.SubsetPolicy.create_graph
        • moscot.utils.subset_policy.SubsetPolicy.create_mask
        • moscot.utils.subset_policy.SubsetPolicy.create_masks
        • moscot.utils.subset_policy.SubsetPolicy.plan
        • moscot.utils.subset_policy.SubsetPolicy.remove_node
        • moscot.utils.subset_policy.SubsetPolicy.categories
        • moscot.utils.subset_policy.SubsetPolicy.key
      • moscot.utils.subset_policy.OrderedPolicy
        • moscot.utils.subset_policy.OrderedPolicy.add_node
        • moscot.utils.subset_policy.OrderedPolicy.create_graph
        • moscot.utils.subset_policy.OrderedPolicy.create_mask
        • moscot.utils.subset_policy.OrderedPolicy.create_masks
        • moscot.utils.subset_policy.OrderedPolicy.plan
        • moscot.utils.subset_policy.OrderedPolicy.remove_node
        • moscot.utils.subset_policy.OrderedPolicy.reverse
        • moscot.utils.subset_policy.OrderedPolicy.categories
        • moscot.utils.subset_policy.OrderedPolicy.key
      • moscot.utils.subset_policy.StarPolicy
        • moscot.utils.subset_policy.StarPolicy.add_node
        • moscot.utils.subset_policy.StarPolicy.create_graph
        • moscot.utils.subset_policy.StarPolicy.create_mask
        • moscot.utils.subset_policy.StarPolicy.create_masks
        • moscot.utils.subset_policy.StarPolicy.plan
        • moscot.utils.subset_policy.StarPolicy.remove_node
        • moscot.utils.subset_policy.StarPolicy.reverse
        • moscot.utils.subset_policy.StarPolicy.categories
        • moscot.utils.subset_policy.StarPolicy.key
        • moscot.utils.subset_policy.StarPolicy.reference
      • moscot.utils.subset_policy.ExternalStarPolicy
        • moscot.utils.subset_policy.ExternalStarPolicy.add_node
        • moscot.utils.subset_policy.ExternalStarPolicy.create_graph
        • moscot.utils.subset_policy.ExternalStarPolicy.create_mask
        • moscot.utils.subset_policy.ExternalStarPolicy.create_masks
        • moscot.utils.subset_policy.ExternalStarPolicy.plan
        • moscot.utils.subset_policy.ExternalStarPolicy.remove_node
        • moscot.utils.subset_policy.ExternalStarPolicy.reverse
        • moscot.utils.subset_policy.ExternalStarPolicy.categories
        • moscot.utils.subset_policy.ExternalStarPolicy.key
        • moscot.utils.subset_policy.ExternalStarPolicy.reference
      • moscot.utils.subset_policy.SequentialPolicy
        • moscot.utils.subset_policy.SequentialPolicy.add_node
        • moscot.utils.subset_policy.SequentialPolicy.create_graph
        • moscot.utils.subset_policy.SequentialPolicy.create_mask
        • moscot.utils.subset_policy.SequentialPolicy.create_masks
        • moscot.utils.subset_policy.SequentialPolicy.plan
        • moscot.utils.subset_policy.SequentialPolicy.remove_node
        • moscot.utils.subset_policy.SequentialPolicy.reverse
        • moscot.utils.subset_policy.SequentialPolicy.categories
        • moscot.utils.subset_policy.SequentialPolicy.key
      • moscot.utils.subset_policy.TriangularPolicy
        • moscot.utils.subset_policy.TriangularPolicy.add_node
        • moscot.utils.subset_policy.TriangularPolicy.create_graph
        • moscot.utils.subset_policy.TriangularPolicy.create_mask
        • moscot.utils.subset_policy.TriangularPolicy.create_masks
        • moscot.utils.subset_policy.TriangularPolicy.plan
        • moscot.utils.subset_policy.TriangularPolicy.remove_node
        • moscot.utils.subset_policy.TriangularPolicy.reverse
        • moscot.utils.subset_policy.TriangularPolicy.categories
        • moscot.utils.subset_policy.TriangularPolicy.key
      • moscot.utils.subset_policy.ExplicitPolicy
        • moscot.utils.subset_policy.ExplicitPolicy.add_node
        • moscot.utils.subset_policy.ExplicitPolicy.create_graph
        • moscot.utils.subset_policy.ExplicitPolicy.create_mask
        • moscot.utils.subset_policy.ExplicitPolicy.create_masks
        • moscot.utils.subset_policy.ExplicitPolicy.plan
        • moscot.utils.subset_policy.ExplicitPolicy.remove_node
        • moscot.utils.subset_policy.ExplicitPolicy.categories
        • moscot.utils.subset_policy.ExplicitPolicy.key
      • moscot.utils.data.transcription_factors
      • moscot.utils.data.proliferation_markers
      • moscot.utils.data.apoptosis_markers
      • moscot.utils.tagged_array.TaggedArray
        • moscot.utils.tagged_array.TaggedArray.from_adata
        • moscot.utils.tagged_array.TaggedArray.cost
        • moscot.utils.tagged_array.TaggedArray.data_tgt
        • moscot.utils.tagged_array.TaggedArray.is_cost_matrix
        • moscot.utils.tagged_array.TaggedArray.is_graph
        • moscot.utils.tagged_array.TaggedArray.is_kernel
        • moscot.utils.tagged_array.TaggedArray.is_point_cloud
        • moscot.utils.tagged_array.TaggedArray.shape
        • moscot.utils.tagged_array.TaggedArray.tag
        • moscot.utils.tagged_array.TaggedArray.data_src
      • moscot.utils.tagged_array.Tag
        • moscot.utils.tagged_array.Tag.encode
        • moscot.utils.tagged_array.Tag.replace
        • moscot.utils.tagged_array.Tag.split
        • moscot.utils.tagged_array.Tag.rsplit
        • moscot.utils.tagged_array.Tag.join
        • moscot.utils.tagged_array.Tag.capitalize
        • moscot.utils.tagged_array.Tag.casefold
        • moscot.utils.tagged_array.Tag.title
        • moscot.utils.tagged_array.Tag.center
        • moscot.utils.tagged_array.Tag.count
        • moscot.utils.tagged_array.Tag.expandtabs
        • moscot.utils.tagged_array.Tag.find
        • moscot.utils.tagged_array.Tag.partition
        • moscot.utils.tagged_array.Tag.index
        • moscot.utils.tagged_array.Tag.ljust
        • moscot.utils.tagged_array.Tag.lower
        • moscot.utils.tagged_array.Tag.lstrip
        • moscot.utils.tagged_array.Tag.rfind
        • moscot.utils.tagged_array.Tag.rindex
        • moscot.utils.tagged_array.Tag.rjust
        • moscot.utils.tagged_array.Tag.rstrip
        • moscot.utils.tagged_array.Tag.rpartition
        • moscot.utils.tagged_array.Tag.splitlines
        • moscot.utils.tagged_array.Tag.strip
        • moscot.utils.tagged_array.Tag.swapcase
        • moscot.utils.tagged_array.Tag.translate
        • moscot.utils.tagged_array.Tag.upper
        • moscot.utils.tagged_array.Tag.startswith
        • moscot.utils.tagged_array.Tag.endswith
        • moscot.utils.tagged_array.Tag.removeprefix
        • moscot.utils.tagged_array.Tag.removesuffix
        • moscot.utils.tagged_array.Tag.isascii
        • moscot.utils.tagged_array.Tag.islower
        • moscot.utils.tagged_array.Tag.isupper
        • moscot.utils.tagged_array.Tag.istitle
        • moscot.utils.tagged_array.Tag.isspace
        • moscot.utils.tagged_array.Tag.isdecimal
        • moscot.utils.tagged_array.Tag.isdigit
        • moscot.utils.tagged_array.Tag.isnumeric
        • moscot.utils.tagged_array.Tag.isalpha
        • moscot.utils.tagged_array.Tag.isalnum
        • moscot.utils.tagged_array.Tag.isidentifier
        • moscot.utils.tagged_array.Tag.isprintable
        • moscot.utils.tagged_array.Tag.zfill
        • moscot.utils.tagged_array.Tag.format
        • moscot.utils.tagged_array.Tag.format_map
        • moscot.utils.tagged_array.Tag.maketrans
        • moscot.utils.tagged_array.Tag.COST_MATRIX
        • moscot.utils.tagged_array.Tag.KERNEL
        • moscot.utils.tagged_array.Tag.POINT_CLOUD
        • moscot.utils.tagged_array.Tag.GRAPH
      • moscot.utils.tagged_array.DistributionCollection
        • moscot.utils.tagged_array.DistributionCollection.clear
        • moscot.utils.tagged_array.DistributionCollection.copy
        • moscot.utils.tagged_array.DistributionCollection.fromkeys
        • moscot.utils.tagged_array.DistributionCollection.get
        • moscot.utils.tagged_array.DistributionCollection.items
        • moscot.utils.tagged_array.DistributionCollection.keys
        • moscot.utils.tagged_array.DistributionCollection.pop
        • moscot.utils.tagged_array.DistributionCollection.popitem
        • moscot.utils.tagged_array.DistributionCollection.setdefault
        • moscot.utils.tagged_array.DistributionCollection.update
        • moscot.utils.tagged_array.DistributionCollection.values
      • moscot.utils.tagged_array.DistributionContainer
        • moscot.utils.tagged_array.DistributionContainer.from_adata
        • moscot.utils.tagged_array.DistributionContainer.contains_condition
        • moscot.utils.tagged_array.DistributionContainer.contains_linear
        • moscot.utils.tagged_array.DistributionContainer.contains_quadratic
        • moscot.utils.tagged_array.DistributionContainer.xy
        • moscot.utils.tagged_array.DistributionContainer.xx
        • moscot.utils.tagged_array.DistributionContainer.a
        • moscot.utils.tagged_array.DistributionContainer.b
        • moscot.utils.tagged_array.DistributionContainer.conditions
        • moscot.utils.tagged_array.DistributionContainer.cost_xy
        • moscot.utils.tagged_array.DistributionContainer.cost_xx
  • Optimal Transport (OT) in a nutshell
  • Tutorials
    • Mapping lineage-traced cells across time points with moslin
    • Disentangling lineage relationships of delta and epsilon cells in pancreatic development with the TemporalProblem
    • Alignment of spatial transcriptomics data
    • Mapping gene expression in space
    • Spatiotemporal trajectory of mouse organogenesis
    • Translating multiomics single-cell data
    • Perturbation modeling with the SinkhornProblem
  • Examples
    • Tagged arrays
    • Passing callbacks in prepare()
    • Custom cost matrices
    • Adding and removing problems
    • Subset policy
    • Handling marginals
    • Annotation mapping
    • Problems
      • Alignment Problem
        • Sequential alignment
      • Lineage Problem
        • Lineage tree
        • Including barcode information via barcode distances
      • Spatio Temporal Problem
        • Creating marginals from proliferation and apoptosis markers in developmental processes
      • Temporal Problem
        • Creating marginals from proliferation and apoptosis markers in developmental processes
    • Linear problems
    • Linear problems (advanced)
    • Quadratic problems
    • Quadratic problems (advanced)
    • Pull/push distributions
    • Cell transitions
    • Sankey diagram
  • Contributing guide
  • References
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Lineage ProblemΒΆ

  • Lineage tree
  • Including barcode information via barcode distances
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