> ## Documentation Index
> Fetch the complete documentation index at: https://docs.scmcphub.org/llms.txt
> Use this file to discover all available pages before exploring further.

# cellrank MCP Server Tools

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

## 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

## 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

## 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