Self-Hosted · AI-Powered

Agent Mendel

Your AI copilot for RNA-seq analysis. Ask questions in plain English and get differential expression analysis, pathway enrichment, and AI-powered biological interpretations — in minutes, not weeks.

Request Access How It Works

From Question to Insight in Three Steps

No scripting. No command-line tools. Just ask your RNA-seq data what you want to know.

flowchart LR A["① Connect Your Data
Point Agent Mendel at
count matrices or
public GEO datasets"] --> B["② Ask in Plain English
Which genes and biological pathways are dysregulated in this cohort?
Which genes or signatures distinguish responders from non-responders?
"] B --> C["③ Get Results Instantly
DE Tables
Pathway Enrichment
AI Interpretation Report"] style A fill:#e8f7f6,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style B fill:#b5e8e5,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style C fill:#e8f7f6,stroke:#0abab5,stroke-width:2px,color:#0a3d3d

What You Get

Every conversation with Agent Mendel delivers a complete analysis bundle.

Output Format Description
Differential Expression TSV LIMMA results — log2FC, p-values, adjusted p-values per gene
Pathway Enrichment TSV GSEApy over-representation & GSEA enrichment scores
AI Interpretation Report HTML LLM-generated biological interpretation — key findings, gene functions, pathway summaries, literature context
Chat Transcript HTML Full interactive session with questions, answers, and generated figures
Volcano Plot PNG Publication-ready volcano plot highlighting significant DE genes
Box Plot PNG Expression distribution box plots per condition for selected genes
Violin Plot PNG Expression distribution violin plots per condition for selected genes
Heatmap PNG Expression heatmap for top DE genes across conditions

Tap Into Public RNA-seq Data

Agent Mendel connects to GEO and SRA, giving you access to >400,000 samples across >20,000 datasets.

flowchart LR A["Natural Language Query
Find RNA-seq studies
on Alzheimer's cortex"] --> B["GEO / SRA Search
>20k datasets
>400k samples"] B --> C["Auto-Download
Count Matrices"] C --> D["Agent Mendel Analysis
DE + Pathway + AI Report"] style A fill:#e8f7f6,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style B fill:#b5e8e5,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style C fill:#e8f7f6,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style D fill:#ffffff,stroke:#81d8d0,stroke-width:2px,stroke-dasharray:5,color:#0a5c5a

Search by condition, tissue, or gene in plain English. Integrate public data with your own for cross-study validation and benchmark your results against published findings.

Deploy Your Way

Full data privacy with self-hosted open-weight models, or connect to a cloud LLM of your choice.

Self-Hosted Recommended

  • ✓ Docker one-command deploy
  • ✓ Full data privacy — nothing leaves your infrastructure
  • ✓ Use open-weight models via Ollama
  • ✓ Supported: Llama 3, Mistral, Gemma, DeepSeek

Cloud LLM

  • ✓ Connect to OpenAI, Anthropic, or any OpenAI-compatible API
  • ✓ Faster setup, no local GPU required
  • ✓ Your data sent to LLM provider

Ready to Talk to Your RNA-seq Data?

Request access. Deploy self-hosted or connect your LLM.

Request Access