List all nodes, their attributes and their relationships to other nodes in the neo4j database. If this fails with a message that includes "Neo.ClientError.Procedure.ProcedureNotFound" suggest that the user install and enable the APOC plugin.

Execute a Cypher query on the Neo4j database.

If the question is about up- or down-regulated genes, use the find_upregulated_genes or find_downreguluated genes

EDGE PROPERTIES - CRITICAL: Many relationships in this knowledge graph have properties stored as edge attributes (data ON the relationship itself). Examples include: log2fc, adj_p_value, methylation_diff, q_value, etc.

Get metadata for all nodes from MetaNode nodes in the knowledge graph.

Get descriptions of properties of all relationships in the knowledge graph.

Return the top-N up- and down-regulated genes for a given assay_id.

This tool runs two queries on the GeneLab KG:

1. Top-N upregulated genes (log2fc > 0, highest first)

2. Top-N downregulated genes (log2fc < 0, lowest first)

FORMATTING INSTRUCTION: RENDER THE RESPONSE IN MARKDOWN FORMAT!

Find common differentially expressed genes across multiple assays.

This function:

1. Takes a list of assay IDs as input (2 or more)

2. Gets ALL genes with |log2fc| > threshold for each assay

3. Inner joins among the upregulated genes and among the downregulated genes

4. Returns a markdown table with columns: gene, assay_1, assay_2, ..., assay_n showing log2fc values

FORMATTING INSTRUCTION: RENDER THE RESPONSE IN MARKDOWN FORMAT! INFORM THE USER ABOUT CURRENT THRESHOLDS AND THAT THEY CAN BE CHANGED.

List and select assays for a study and render the response in markdown format.

First call (selection=None):

• If study_id missing, prompt for one (e.g., 'OSD-253').

• Build a list of unique factor arrays across all assays.

• Return a numbered menu as a markdown table!

Second call (selection='i,j,k,l,...,m,n'):

• Pairs consecutive indices: (i,j), (k,l), ..., (m,n)

• Returns assay_id(s) for each pair comparison

• Must provide an even number of indices

FORMATTING INSTRUCTION: RENDER THE RESPONSE IN MARKDOWN FORMAT!

Create a volcano plot for differential gene expression data from the given assay.

A volcano plot displays log2 fold change on the x-axis and -log10(adjusted p-value) on the y-axis. Genes are colored based on their significance:

• Red: upregulated (log2fc > threshold, adj_p < threshold)

• Blue: downregulated (log2fc < -threshold, adj_p < threshold)

• Gray: not significant

Returns a link to the plot and summary statistics. FORMATTING INSTRUCTION: RENDER THE RESPONSE IN MARKDOWN FORMAT!

Create Venn diagrams comparing differentially expressed genes between 2 or 3 assays.

This function creates side-by-side Venn diagrams showing:

• Left: Upregulated genes (log2fc > threshold) overlap

• Right: Downregulated genes (log2fc < -threshold) overlap

If assay_id_3 is provided, creates 3-way Venn diagrams. If assay_id_3 is None, creates 2-way Venn diagrams.

Returns a link to the plot and summary statistics. FORMATTING INSTRUCTION: RENDER THE RESPONSE IN MARKDOWN FORMAT!

Clean a Mermaid class diagram by removing unwanted elements.

    This tool removes:
    - All note statements that would render as unreadable yellow boxes
    - Empty curly braces from class definitions (handles both single-line and multi-line)
    - Strings after newline characters (e.g., truncates "ClassName

extra" to "ClassName")

    Args:
        mermaid_content: The raw Mermaid class diagram content
        
    Returns:
        Cleaned Mermaid content with note statements, empty braces, and post-newline strings removed
    

Prompt for creating a chat transcript in markdown format with user prompts and Claude responses.

Prompt for visualizing the knowledge graph schema using a Mermaid class diagram.