Cytomulate: Accurate and Efficient Simulation of CyTOF data

Cytomulate is a package to simulation realistic data for Mass Cytometry or Cytometry by Time-of-Flight (CyTOF). We support both model-based through Creation Mode and real-data-based simulation through Emulation Mode. Cytomulate serves as solutions to benchmarking, method validation, prototyping, and more. You can easily generate realistic and accurately CyTOF simulations within seconds.

Using our unified framework compatible with PyCytoData, you can stay within our ecosystem: starting from simulation to precessing, you can then select the best dimension reduction method for your dataset and proceed onto other downstream analyses. All you need is a few simple commands! For more details, read our tutorials and documentations linked below! Or try this example:

>>> from cytomulate import CreationCytofData

>>> cytof_data = CreationCytofData()
>>> cytof_data.initialize_cell_types()
>>> expression_matrices, labels, _, _ = cytof_data.sample(n_samples = 100)

When in doubt, Cytomulate it!

Full API Reference


For our paper, read our preprint here.

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