paga
Partition-based Graph Abstraction tool for single-cell RNA sequencing analysis. Abstracts cell populations into graphs, identifies clusters, and models connectivity using RNA velocity or predefined groups.
Instructions
Partition-based graph abstraction
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| groups | No | Key for categorical in adata.obs. You can pass your predefined groups by choosing any categorical annotation of observations. Default: The first present key of 'leiden' or 'louvain'. | |
| model | No | The PAGA connectivity model. | v1.2 |
| neighbors_key | No | If specified, paga looks .uns[neighbors_key] for neighbors settings and uses the corresponding connectivities and distances. | |
| use_rna_velocity | No | Use RNA velocity to orient edges in the abstracted graph and estimate transitions. Requires that adata.uns contains a directed single-cell graph with key ['velocity_graph']. |
Input Schema (JSON Schema)
{
"description": "Input schema for the Partition-based Graph Abstraction (PAGA) tool.",
"properties": {
"groups": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Key for categorical in adata.obs. You can pass your predefined groups by choosing any categorical annotation of observations. Default: The first present key of 'leiden' or 'louvain'.",
"title": "Groups"
},
"model": {
"default": "v1.2",
"description": "The PAGA connectivity model.",
"enum": [
"v1.2",
"v1.0"
],
"title": "Model",
"type": "string"
},
"neighbors_key": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "If specified, paga looks .uns[neighbors_key] for neighbors settings and uses the corresponding connectivities and distances.",
"title": "Neighbors Key"
},
"use_rna_velocity": {
"default": false,
"description": "Use RNA velocity to orient edges in the abstracted graph and estimate transitions. Requires that adata.uns contains a directed single-cell graph with key ['velocity_graph'].",
"title": "Use Rna Velocity",
"type": "boolean"
}
},
"title": "PAGAModel",
"type": "object"
}