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developer.rst
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developer.rst
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Developer API
#############
Backends
~~~~~~~~
.. module:: moscot.backends
.. currentmodule:: moscot
.. autosummary::
:toctree: genapi
backends.ott.SinkhornSolver
backends.ott.GWSolver
backends.ott.OTTOutput
backends.ott.GraphOTTOutput
backends.utils.get_solver
backends.utils.get_available_backends
Costs
~~~~~
.. module:: moscot.costs
.. currentmodule:: moscot
.. autosummary::
:toctree: genapi
costs.BarcodeDistance
costs.LeafDistance
costs.get_cost
costs.get_available_costs
costs.register_cost
Base
~~~~
.. module:: moscot.base
.. currentmodule:: moscot.base
Problems
^^^^^^^^
.. autosummary::
:toctree: genapi
problems.BaseProblem
problems.OTProblem
problems.BirthDeathProblem
problems.BaseCompoundProblem
problems.CompoundProblem
cost.BaseCost
Mixins
^^^^^^
.. autosummary::
:toctree: genapi
problems.AnalysisMixin
problems.BirthDeathMixin
Solvers
^^^^^^^
.. module:: moscot.solvers
.. currentmodule:: moscot.base
.. autosummary::
:toctree: genapi
solver.BaseSolver
solver.OTSolver
output.BaseSolverOutput
Output
^^^^^^
.. autosummary::
:toctree: genapi
output.BaseSolverOutput
output.MatrixSolverOutput
Utils
~~~~~
.. module:: moscot.utils
.. currentmodule:: moscot.utils
Policies
^^^^^^^^
.. autosummary::
:toctree: genapi
subset_policy.SubsetPolicy
subset_policy.OrderedPolicy
subset_policy.StarPolicy
subset_policy.ExternalStarPolicy
subset_policy.SequentialPolicy
subset_policy.TriangularPolicy
subset_policy.ExplicitPolicy
Miscellaneous
^^^^^^^^^^^^^
.. autosummary::
:toctree: genapi
data.transcription_factors
data.proliferation_markers
data.apoptosis_markers
tagged_array.TaggedArray
tagged_array.Tag
.. currentmodule:: moscot.base.problems
.. autosummary::
:toctree: genapi
birth_death.beta
birth_death.delta