dpt
Perform Diffusion Pseudotime (DPT) analysis on single-cell RNA sequencing data to identify developmental trajectories and branchings using configurable parameters such as diffusion components and group size thresholds.
Instructions
Diffusion Pseudotime (DPT) analysis
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| allow_kendall_tau_shift | No | If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion to stabilize the splitting. | |
| min_group_size | No | During recursive splitting of branches, do not consider groups that contain less than min_group_size data points. If a float, refers to a fraction of the total number of data points. | |
| n_branchings | No | Number of branchings to detect. | |
| n_dcs | No | The number of diffusion components to use. | |
| neighbors_key | No | If specified, dpt looks .uns[neighbors_key] for neighbors settings and uses the corresponding connectivities and distances. |
Input Schema (JSON Schema)
{
"description": "Input schema for the Diffusion Pseudotime (DPT) tool.",
"properties": {
"allow_kendall_tau_shift": {
"default": true,
"description": "If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion to stabilize the splitting.",
"title": "Allow Kendall Tau Shift",
"type": "boolean"
},
"min_group_size": {
"default": 0.01,
"description": "During recursive splitting of branches, do not consider groups that contain less than min_group_size data points. If a float, refers to a fraction of the total number of data points.",
"exclusiveMinimum": 0,
"maximum": 1,
"title": "Min Group Size",
"type": "number"
},
"n_branchings": {
"default": 0,
"description": "Number of branchings to detect.",
"minimum": 0,
"title": "N Branchings",
"type": "integer"
},
"n_dcs": {
"default": 10,
"description": "The number of diffusion components to use.",
"exclusiveMinimum": 0,
"title": "N Dcs",
"type": "integer"
},
"neighbors_key": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "If specified, dpt looks .uns[neighbors_key] for neighbors settings and uses the corresponding connectivities and distances.",
"title": "Neighbors Key"
}
},
"title": "DPTModel",
"type": "object"
}