---
title: "Genomics & Multi-Omics overview"
description: "Cluster and annotate single-cell RNA-seq, find differentially expressed genes, map pathway enrichment, and get from a disease signal to a druggable target."
tags:
  - section
  - genomics-omics
generated: true
---

Upstream of chemistry sits biology: which target should you drug at all? This section analyzes bulk and single-cell omics to find differentially expressed genes, map pathways, and nominate druggable targets from disease data. It's how a program gets from a disease to a target worth a structure.

> **Availability**

> These tools are metered by credits and gated by your plan — plans set your monthly credits, available model families, and which modal-app tools you can run. See [Plans & tiers](/docs/plans-and-tiers).

## What you can achieve here

- Analyze single-cell RNA-seq — cluster, annotate, differential expression
- Integrate multi-omics layers
- Go from a disease signal to a druggable target
- Map pathways and enrichment

For which tool fits each, see [What you can achieve](/docs/capabilities).

## Tools in this section

| Tool | What it does |
|---|---|
| [Genomics on the platform](/docs/genomics) | Multi-database genomics query tools for gene information, pathway analysis, variant interpretation, and cross-database linking. |
| [Epigenomics on the platform](/docs/epigenomics) | Chromatin accessibility, histone modification, and DNA methylation analysis tools for epigenomic profiling. |
| [Metagenomics on the platform](/docs/metagenomics) | Taxonomic classification, community profiling, diversity analysis, and differential abundance tools for microbiome and metagenomic studies. |
| [Causal Genomics on the platform](/docs/causal-genomics) | Statistical genetics tools for Mendelian randomization, fine-mapping, colocalization, and LD score regression to find causal variants. |
| [Scanpy on the platform](/docs/scanpy) | Single-cell RNA-seq analysis with Scanpy for preprocessing, clustering, and trajectory inference. |
| [scvi-tools on the platform](/docs/scvi-tools) | Deep generative models for single-cell RNA-seq analysis including batch correction, cell type annotation, doublet detection, and multi-modal… |
| [Spatial Omics on the platform](/docs/spatial-omics) | Estimate cell type proportions per Visium spot with spatial_deconvolve and a required scRNA-seq reference; the communication and domain tools are… |
| [Proteomics on the platform](/docs/proteomics) | Search PRIDE mass spectrometry datasets and EMDB cryo-EM structures for protein identification, quantification, and structural analysis. |
| [Metabolomics on the platform](/docs/metabolomics) | Metabolomics data preprocessing, metabolite annotation, differential analysis, and pathway enrichment tools for mass spectrometry workflows. |
| [Transformers](/docs/transformers) | Not currently callable. No embedding or cross-modal tool replaces it; run your own model in the sandbox. |

## Recipes using these tools

## Read next