Developer API

Backends

backends.ott.SinkhornSolver([jit, rank, ...])	Solver for the linear problem.
backends.ott.GWSolver([jit, rank, ...])	Solver for the quadratic problem [Mémoli, 2011].
backends.ott.OTTOutput(output)	Output of various OT problems.
backends.ott.GraphOTTOutput(output, shape)	Output of OT problems with a graph geometry in the linear term.
backends.utils.get_solver(problem_kind, *[, ...])	TODO.
backends.utils.get_available_backends()	Return all available backends.

Costs

costs.BarcodeDistance(adata, **kwargs)	Scaled Hamming distance between barcodes.
costs.LeafDistance(adata[, weight])	Shortest path distance on a weighted tree.
costs.get_cost(name, *[, backend])	Get cost function for a specific backend.
costs.get_available_costs([backend])	Return available costs.
costs.register_cost(name, *, backend)	Register cost function for a specific backend.

Base

Problems

problems.BaseProblem()	Base class for all OT problems.
problems.OTProblem(adata[, adata_tgt, ...])	Base class for all OT problems.
problems.BirthDeathProblem(*args, **kwargs)	OT problem used to estimate the marginals with the birth-death process.
problems.BaseCompoundProblem(adata, **kwargs)	Base class for all biological problems.
problems.CompoundProblem(adata, **kwargs)	Base class for all biological problems.
cost.BaseCost(adata, attr, key[, dist_key])	Base class for moscot.costs.

Mixins

problems.AnalysisMixin(*args, **kwargs)	Base Analysis Mixin.
problems.BirthDeathMixin(*args, **kwargs)	Mixin class used to estimate cell proliferation and apoptosis.

Solvers

solver.BaseSolver()	Base class for all solvers.
solver.OTSolver()	Base class for optimal transport solvers.
output.BaseSolverOutput()	Base class for all solver outputs.

Output

output.BaseSolverOutput()	Base class for all solver outputs.
output.MatrixSolverOutput(transport_matrix, *)	OT solution with a materialized transport matrix.

Utils

Policies

subset_policy.SubsetPolicy(adata[, key, ...])	Base policy class.
subset_policy.OrderedPolicy(adata[, key, ...])	Base ordered policy.
subset_policy.StarPolicy(adata[, key, ...])	Policy with a star topology.
subset_policy.ExternalStarPolicy(adata[, ...])	Policy with star topology and external central node.
subset_policy.SequentialPolicy(adata[, key, ...])	Policy which connects immediate successors.
subset_policy.TriangularPolicy(adata[, upper])	Policy which connects all preceding/subsequent nodes.
subset_policy.ExplicitPolicy(adata[, key, ...])	Explicitly specified policy.

Miscellaneous

data.transcription_factors(organism)	Get transcription factors for a selected organism.
data.proliferation_markers(organism)	Get proliferation markers for a selected organism.
data.apoptosis_markers(organism)	Get apoptosis markers for a selected organism.
tagged_array.TaggedArray(data_src[, ...])	Interface to interpret array-like data for moscot.solvers.
tagged_array.Tag(value)	Tag in the TaggedArray.

birth_death.beta(p[, beta_max, beta_min, ...])	Birth process.
birth_death.delta(a[, delta_max, delta_min, ...])	Death process.