---
title: "Discover Targets From Omics"
description: "Discover Targets From Omics: an analysis recipe chaining scanpy."
tags:
  - recipes
  - analysis
tools:
  - scanpy
generated: true
source: quickActionConfig:omics-to-target
---

> **Generated recipe**

> Seeded from a curated quick-action prompt. The prompt below runs the real
> routing — copy it, change the target, and run.

**Best fit:** discover targets from omics — an analysis goal.

**Try this prompt** — [open in a guest chat](/chat/new?guest=true&prompt=hf_arc_se_167m_human).

> hf_arc_se_167m_human

_A real `omics-to-target` quick-action prompt — open it in a guest chat, then swap in your own compound or target._

## The prompt

```text
Slice a COVID-19 PBMC severe-vs-healthy cohort out of Arc Institute SE-167M-Human single-cell RNA atlas (167M human cells across tissues) (Hugging Face arcinstitute/SE-167M-Human; datasets.load_dataset('arcinstitute/SE-167M-Human', streaming=True) — slice by tissue/disease metadata before materialising.) (HF streaming loader, filter on disease + tissue=PBMC), analyse with Scanpy: cluster to identify cell types, run DE between COVID-severe vs healthy for each cluster, annotate top markers with MyGene.info, check OpenTargets for druggability, and query DGIdb for existing drugs targeting DE genes - which cell-type-specific markers are druggable, and do the hyperinflammatory monocyte markers suggest repurposing opportunities for approved JAK inhibitors or anti-IL-6 antibodies?
```

## What each tool contributes

- [scanpy](/docs/scanpy) — Single-cell clustering, DE analysis, marker gene identification
- **mygene query** — Gene annotations, pathways, and cross-references
- **opentargets associations** — Disease-target association scores

## Why these tools pair

Scanpy identifies marker genes, MyGene annotates them, OpenTargets assesses disease relevance — data-driven target discovery pipeline

## Data flow

Every tool operates on the same input: `gene_list`.

## Read next

- [Which tool?](/docs/which-tool) — match a single goal to a tool.
- [Workflows](/docs/workflows) — every workflow and recipe.
- [How the orchestrator picks tools](/docs/how-orchestration-works) — the same chain from a plain-language goal.