Genomics & Multi-Omics overview
Cluster and annotate single-cell RNA-seq, find differentially expressed genes, map pathway enrichment, and get from a disease signal to a druggable target.
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.
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.
Tools in this section
| Tool | What it does |
|---|---|
| Genomics on the platform | Multi-database genomics query tools for gene information, pathway analysis, variant interpretation, and cross-database linking. |
| Epigenomics on the platform | Chromatin accessibility, histone modification, and DNA methylation analysis tools for epigenomic profiling. |
| Metagenomics on the platform | Taxonomic classification, community profiling, diversity analysis, and differential abundance tools for microbiome and metagenomic studies. |
| Causal Genomics on the platform | Statistical genetics tools for Mendelian randomization, fine-mapping, colocalization, and LD score regression to find causal variants. |
| Scanpy on the platform | Single-cell RNA-seq analysis with Scanpy for preprocessing, clustering, and trajectory inference. |
| scvi-tools on the platform | 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 | 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 | Search PRIDE mass spectrometry datasets and EMDB cryo-EM structures for protein identification, quantification, and structural analysis. |
| Metabolomics on the platform | Metabolomics data preprocessing, metabolite annotation, differential analysis, and pathway enrichment tools for mass spectrometry workflows. |
| Transformers | Not currently callable. No embedding or cross-modal tool replaces it; run your own model in the sandbox. |
Recipes using these tools
Find Binding Motifs
Find Binding Motifs: an epigenomics recipe chaining epigenomics.
Annotate Metabolome
Annotate Metabolome: an omics recipe chaining metabolomics, metabolomics.
Discover Targets From Omics
Discover Targets From Omics: an analysis recipe chaining scanpy.
Analyze Single-Cell Data
Analyze Single-Cell Data: a genomics recipe chaining scanpy.
Read next
What you can achieve
The outcomes these tools deliver — and which to pick when several do the same thing.
Which tool?
Match a scientific goal to a tool across every domain.
Concept clusters
How tools, jobs, and results fit together.
Workflows
Guided pipelines and copy-and-adapt prompt recipes for common goals.
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AAV quickstart
Name a target tissue for per-serotype tropism reports with citations and no ranking, then codon-optimize a protein transgene against the 4.7 kb limit.
Genomics on the platform
Multi-database genomics query tools for gene information, pathway analysis, variant interpretation, and cross-database linking.