scAgent/tools/cellchat.json at main · deepmind11/scAgent · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
{
  "tool_id": "cellchat",
  "name": "CellChat Cell-Cell Communication",
  "category": "communication",
  "framework": "cellchat",
  "function": "CellChat (R via subprocess)",
  "valid_after": [
    "annotation"
  ],
  "valid_before": [],
  "paradigms": [
    "cell_atlas",
    "disease_vs_healthy",
    "developmental_trajectory"
  ],
  "parameters": {
    "cell_type_key": {
      "type": "string",
      "required": true,
      "guidance": "obs column with cell type annotations."
    },
    "db_type": {
      "type": "string",
      "default": "CellChatDB.human",
      "options": [
        "CellChatDB.human",
        "CellChatDB.mouse"
      ],
      "guidance": "Ligand-receptor database. Match to species."
    },
    "min_cells": {
      "type": "int",
      "default": 10,
      "guidance": "Minimum cells per cell type to include in analysis."
    },
    "signaling_type": {
      "type": "string",
      "default": "all",
      "options": [
        "all",
        "Secreted_Signaling",
        "ECM-Receptor",
        "Cell-Cell_Contact"
      ],
      "guidance": "Filter to specific signaling categories."
    }
  },
  "outputs": {
    "communication_network": "Significant ligand-receptor interactions between cell types",
    "signaling_pathways": "Active signaling pathways per cell type pair",
    "n_significant_interactions": "int"
  },
  "validation": {
    "check": "At least some significant interactions found. No interactions may indicate too few cells or misannotated cell types."
  },
  "provenance_captures": [
    "cell_type_key",
    "db_type",
    "min_cells",
    "signaling_type",
    "n_cell_types",
    "n_significant_interactions"
  ]
}