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moscot documentation
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  • Installation
  • User guide
  • User API
    • 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
    • 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
    • moscot.problems.generic.GENOTLinProblem
      • moscot.problems.generic.GENOTLinProblem.cell_transition
      • moscot.problems.generic.GENOTLinProblem.compute_entropy
      • moscot.problems.generic.GENOTLinProblem.compute_feature_correlation
      • moscot.problems.generic.GENOTLinProblem.load
      • moscot.problems.generic.GENOTLinProblem.prepare
      • moscot.problems.generic.GENOTLinProblem.pull
      • moscot.problems.generic.GENOTLinProblem.push
      • moscot.problems.generic.GENOTLinProblem.save
      • moscot.problems.generic.GENOTLinProblem.solve
      • moscot.problems.generic.GENOTLinProblem.adata
      • moscot.problems.generic.GENOTLinProblem.batch_key
      • moscot.problems.generic.GENOTLinProblem.distributions
      • moscot.problems.generic.GENOTLinProblem.policy
      • moscot.problems.generic.GENOTLinProblem.problem_kind
      • moscot.problems.generic.GENOTLinProblem.solution
      • moscot.problems.generic.GENOTLinProblem.solver
      • moscot.problems.generic.GENOTLinProblem.stage
    • moscot.plotting.cell_transition
    • moscot.plotting.sankey
    • moscot.plotting.push
    • moscot.plotting.pull
    • 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
    • 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.ott.GENOTLinSolver
      • moscot.backends.ott.GENOTLinSolver.__call__
      • moscot.backends.ott.GENOTLinSolver.problem_kind
      • moscot.backends.ott.GENOTLinSolver.solver
    • moscot.backends.ott.output.OTTNeuralOutput
      • moscot.backends.ott.output.OTTNeuralOutput.as_linear_operator
      • moscot.backends.ott.output.OTTNeuralOutput.chain
      • moscot.backends.ott.output.OTTNeuralOutput.project_to_transport_matrix
      • moscot.backends.ott.output.OTTNeuralOutput.pull
      • moscot.backends.ott.output.OTTNeuralOutput.push
      • moscot.backends.ott.output.OTTNeuralOutput.sparsify
      • moscot.backends.ott.output.OTTNeuralOutput.to
      • moscot.backends.ott.output.OTTNeuralOutput.a
      • moscot.backends.ott.output.OTTNeuralOutput.b
      • moscot.backends.ott.output.OTTNeuralOutput.converged
      • moscot.backends.ott.output.OTTNeuralOutput.cost
      • moscot.backends.ott.output.OTTNeuralOutput.dtype
      • moscot.backends.ott.output.OTTNeuralOutput.is_linear
      • moscot.backends.ott.output.OTTNeuralOutput.is_low_rank
      • moscot.backends.ott.output.OTTNeuralOutput.logs
      • moscot.backends.ott.output.OTTNeuralOutput.potentials
      • moscot.backends.ott.output.OTTNeuralOutput.rank
      • moscot.backends.ott.output.OTTNeuralOutput.shape
      • moscot.backends.ott.output.OTTNeuralOutput.transport_matrix
    • moscot.backends.utils.get_solver
    • moscot.backends.utils.get_available_backends
    • 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
    • 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.CondOTProblem
      • moscot.base.problems.CondOTProblem.load
      • moscot.base.problems.CondOTProblem.prepare
      • moscot.base.problems.CondOTProblem.save
      • moscot.base.problems.CondOTProblem.solve
      • moscot.base.problems.CondOTProblem.adata
      • moscot.base.problems.CondOTProblem.distributions
      • moscot.base.problems.CondOTProblem.policy
      • moscot.base.problems.CondOTProblem.problem_kind
      • moscot.base.problems.CondOTProblem.solution
      • moscot.base.problems.CondOTProblem.solver
      • moscot.base.problems.CondOTProblem.stage
    • moscot.base.problems.AnalysisMixin
      • moscot.base.problems.AnalysisMixin.compute_entropy
      • moscot.base.problems.AnalysisMixin.compute_feature_correlation
    • moscot.base.problems.BirthDeathMixin
      • moscot.base.problems.BirthDeathMixin.score_genes_for_marginals
      • moscot.base.problems.BirthDeathMixin.apoptosis_key
      • moscot.base.problems.BirthDeathMixin.proliferation_key
    • 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.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.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.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
    • moscot.base.problems.birth_death.beta
    • moscot.base.problems.birth_death.delta
  • Contributing guide
  • Tutorials
    • Mapping lineage-traced cells across time points with moslin
    • Analyzing HSPCs 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
    • Lineage tree
    • Including barcode information via barcode distances
    • Creating marginals from proliferation and apoptosis markers in developmental processes
    • Annotation mapping
    • Linear problems
    • Linear problems (advanced)
    • Quadratic problems
    • Quadratic problems (advanced)
    • Pull/push distributions
    • Cell transitions
    • Sankey diagram
  • References
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moscot.base.problems.BirthDeathProblem.y¶

property BirthDeathProblem.y: TaggedArray | None¶

Geometry defining the target quadratic term.

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    • BirthDeathProblem.y