Scxa Tools

Configuration File: scxa_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

SCXA_get_cluster_marker_genes (Type: SCExpressionAtlasTool)

Get EBI Single Cell Expression Atlas computed marker genes per cell cluster (or per cell type) fo…

SCXA_get_cluster_marker_genes tool specification

Tool Information:

  • Name: SCXA_get_cluster_marker_genes

  • Type: SCExpressionAtlasTool

  • Description: Get EBI Single Cell Expression Atlas computed marker genes per cell cluster (or per cell type) for an experiment - results that SCXA_list_experiments and SCXA_search_gene cannot retrieve. marker_type=’clusters’ (default): top marker genes per cell cluster at clustering resolution k (requires k); each row has geneName, the cell-group it marks, expression value, p-value, and unit (CPM). marker_type=’cell_types’: marker genes for inferred cell types (requires organism_part). Example: E-MTAB-5061 k=8 -> rows like {gene_name: ENSG00000224981, cell_group_value_where_marker: ‘1’, p_value: 4.37e-71, expression_unit: CPM}. E-ENAD-13 k=4 -> Olfm4 p_value 3.0e-179.

Parameters:

  • experiment_accession (string) (required) SCXA experiment accession (e.g. ‘E-MTAB-5061’, ‘E-ENAD-13’, ‘E-CURD-4’). Use SCXA_list_experiments to find accessions.

  • marker_type (string) (optional) ‘clusters’ for marker genes per cluster at resolution k (default); ‘cell_types’ for marker genes per inferred cell type (requires organism_part).

  • k (integer) (optional) Clustering resolution / number of clusters for marker_type=’clusters’ (e.g. 8, 4, 6). Required for clusters mode.

  • organism_part (string) (optional) Organism part for marker_type=’cell_types’ (e.g. ‘pancreas’, ‘lung’). Required for cell_types mode.

  • limit (integer) (optional) Optional maximum number of marker rows to return.

Example Usage:

query = {
    "name": "SCXA_get_cluster_marker_genes",
    "arguments": {
        "experiment_accession": "example_value"
    }
}
result = tu.run(query)

SCXA_list_experiments (Type: SCExpressionAtlasTool)

List single-cell RNA-seq experiments from EBI Single Cell Expression Atlas. Returns 380+ curated …

SCXA_list_experiments tool specification

Tool Information:

  • Name: SCXA_list_experiments

  • Type: SCExpressionAtlasTool

  • Description: List single-cell RNA-seq experiments from EBI Single Cell Expression Atlas. Returns 380+ curated scRNA-seq datasets with species, cell counts, technology (10x, Smart-seq2, Drop-seq), and experimental factors (cell type, tissue, disease). Filter by species or keyword. Covers Human Cell Atlas, GTEx, Tabula Sapiens, and more. Example: filtering by ‘Homo sapiens’ returns 159 experiments.

Parameters:

  • species (string) (optional) Species name to filter by (e.g., ‘Homo sapiens’, ‘Mus musculus’, ‘Drosophila melanogaster’). Case-insensitive.

  • keyword (string) (optional) Keyword to search in experiment descriptions and factors (e.g., ‘pancreas’, ‘brain’, ‘cancer’, ‘immune’).

  • limit (integer) (optional) Maximum number of experiments to return (default 20, max 100).

Example Usage:

query = {
    "name": "SCXA_list_experiments",
    "arguments": {
    }
}
result = tu.run(query)

SCXA_search_gene (Type: SCExpressionAtlasTool)

Search the EBI Single Cell Expression Atlas for single-cell experiments where a specific gene is …

SCXA_search_gene tool specification

Tool Information:

  • Name: SCXA_search_gene

  • Type: SCExpressionAtlasTool

  • Description: Search the EBI Single Cell Expression Atlas for single-cell experiments where a specific gene is expressed. Accepts gene symbols (TP53, BRCA1) or Ensembl IDs (ENSG00000141510). Returns matching scRNA-seq experiments with cell counts, technology, PubMed IDs, and DOIs. Useful for finding single-cell datasets studying a gene of interest. Example: TP53 returns 15 experiments including ovarian cancer, lung atlas datasets.

Parameters:

  • gene (string) (required) Gene symbol (e.g., ‘TP53’, ‘BRCA1’, ‘INS’) or Ensembl gene ID (e.g., ‘ENSG00000141510’).

  • species (string) (optional) Species name to filter (e.g., ‘Homo sapiens’, ‘Mus musculus’). Optional.

Example Usage:

query = {
    "name": "SCXA_search_gene",
    "arguments": {
        "gene": "example_value"
    }
}
result = tu.run(query)