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.