Liana Tools

Configuration File: remote_tools/liana_tools.json Tool Type: Remote Tools Count: 1

This page contains all tools defined in the liana_tools.json configuration file.

Available Tools

run_liana_cellphonedb (Type: RemoteTool)

Infer cell-cell communication from a single-cell RNA-seq dataset using LIANA (LIgand-receptor ANa…

run_liana_cellphonedb tool specification

Tool Information:

  • Name: run_liana_cellphonedb

  • Type: RemoteTool

  • Description: Infer cell-cell communication from a single-cell RNA-seq dataset using LIANA (LIgand-receptor ANalysis frAmework; Dimitrov et al., Nature Communications 2022) with its CellPhoneDB permutation-test method, returning the top ligand-receptor interactions between cell types. LIANA is the consensus framework that re-implements CellPhoneDB/CellChat/NATMI/Connectome/etc. over shared curated resources. Input is a server-accessible .h5ad of log1p-normalized expression with a cell-type label column in obs. Each interaction is scored by magnitude (lr_means) and specificity (cellphone_pvals).

Parameters:

  • adata_path (string) (required) Server-accessible path or URL to an .h5ad AnnData of LOG1P-NORMALIZED expression.

  • cluster_key (string) (required) obs column holding the cell-type / cluster labels to compute interactions between.

  • top_n (integer) (optional) Number of top interactions to return, ranked by specificity then magnitude (default 50).

  • expr_prop (number) (optional) Minimum fraction of cells in a group expressing a gene for it to be considered (default 0.1).

Example Usage:

query = {
    "name": "run_liana_cellphonedb",
    "arguments": {
        "adata_path": "example_value",
        "cluster_key": "example_value"
    }
}
result = tu.run(query)