Here is doc for cellrank-mcp, but you can refer to cellrank docs at https://cellrank.readthedocs.io/

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Kernel Module

  • create_kernel: Create a CellRank kernel based on the specified type (pseudotime, cytotrace, velocity, connectivity, realtime)
  • compute_transition_matrix: Compute transition matrix for a specified kernel using appropriate parameters

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Estimator Module

  • create_and_fit_gpcca: Create and fit a Generalized Perron Cluster Cluster Analysis (GPCCA) estimator to compute macrostates
  • predict_terminal_states: Predict terminal states from macrostates
  • predict_initial_states: Compute initial states from macrostates using coarse stationary distribution
  • compute_fate_probabilities: Compute fate probabilities for cells based on terminal states

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Plotting Module

  • kernel_projection: Plot transition matrix as a stream or grid plot for a specified kernel
  • circular_projection: Visualize fate probabilities in a circular embedding