Archs4 Tools

Configuration File: archs4_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the archs4_tools.json configuration file.

Available Tools

ARCHS4_get_gene_correlations (Type: ARCHS4Tool)

Get genes most co-expressed with a query gene from ARCHS4, based on Pearson correlation computed …

ARCHS4_get_gene_correlations tool specification

Tool Information:

  • Name: ARCHS4_get_gene_correlations

  • Type: ARCHS4Tool

  • Description: Get genes most co-expressed with a query gene from ARCHS4, based on Pearson correlation computed across 300K+ uniformly processed RNA-seq samples. Returns the top N most correlated genes with their Pearson correlation coefficients. Useful for identifying functionally related genes, predicting gene function, and building co-expression networks.

Parameters:

  • gene (string) (required) Gene symbol (e.g., TP53, BRCA1, EGFR, MYC)

  • count ([‘integer’, ‘null’]) (optional) Number of top correlated genes to return (default: 20, max: 200)

Example Usage:

query = {
    "name": "ARCHS4_get_gene_correlations",
    "arguments": {
        "gene": "example_value"
    }
}
result = tu.run(query)

ARCHS4_get_gene_expression (Type: ARCHS4Tool)

Get gene expression levels across human or mouse tissues and cell lines from ARCHS4 (All RNA-seq …

ARCHS4_get_gene_expression tool specification

Tool Information:

  • Name: ARCHS4_get_gene_expression

  • Type: ARCHS4Tool

  • Description: Get gene expression levels across human or mouse tissues and cell lines from ARCHS4 (All RNA-seq and ChIP-seq Sample and Signature Search). Returns box-plot statistics (min, Q1, median, Q3, max) in log2(TPM+1) units for each tissue/cell line, computed from 300K+ uniformly processed RNA-seq samples. Choose type=’tissue’ for organ/tissue expression or type=’cellline’ for cell line expression. Results are sorted by median expression (highest first).

Parameters:

  • gene (string) (required) Gene symbol (e.g., TP53, BRCA1, EGFR, MYC)

  • species ([‘string’, ‘null’]) (optional) Species: human or mouse (default: human)

  • type ([‘string’, ‘null’]) (optional) Expression type: tissue (organs/tissues) or cellline (cell lines). Default: tissue

Example Usage:

query = {
    "name": "ARCHS4_get_gene_expression",
    "arguments": {
        "gene": "example_value"
    }
}
result = tu.run(query)