knowledge-work-bio-research

---
name: knowledge-work-bio-research
description: Use when accelerating early-stage life sciences R&D with preclinical tools for literature search, genomics analysis, and drug target prioritization.
source: https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research
generated: 2026-07-02T18:42:03.623Z
category: concept
audience: general
---

## When to use

- Running QC on scRNA-seq data and then integrating or batch-correcting with deep-learning models
- Running nf-core sequencing pipelines (RNA-seq, variant calling, ATAC-seq) on local or public GEO/SRA data
- Searching biomedical literature and prioritizing drug targets for early discovery
- Converting lab instrument output files to a standard Allotrope Simple Model format

## Key concepts

### single-cell-rna-qc skill

Automated QC for scRNA-seq following scverse best practices, supporting .h5ad and .h5 files with MAD-based filtering and visualizations.

### scvi-tools skill

Deep-learning toolkit for single-cell omics covering scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, and sysVI for integration, batch correction, label transfer, and multi-modal analysis.

### nextflow-development skill

Runs nf-core bioinformatics pipelines including rnaseq (differential expression), sarek (germline/somatic variant calling), and atacseq (chromatin accessibility).

### instrument-data-to-allotrope skill

Converts instrument output (PDF, CSV, Excel, TXT) to Allotrope Simple Model format across 40+ instrument types like plate readers, qPCR, and chromatography systems.

### scientific-problem-selection skill

A systematic research problem-selection framework based on Fischbach & Walsh, covering ideation, risk assessment, optimization, decision trees, and synthesis.

### 11 MCP integrations

Bundles data sources including NLM literature, bioRxiv/medRxiv, Consensus, OpenTargets, clinical trial registries, BioRender, and Benchling for research workflows.

## API reference

```
/plugin marketplace add anthropics/knowledge-work-plugins
```

Add Anthropic's knowledge-work plugin marketplace (one-time).

```
/plugin marketplace add anthropics/knowledge-work-plugins
```

```
/plugin install bio-research@knowledge-work-plugins
```

Install the Bio-Research plugin.

```
/plugin install bio-research@knowledge-work-plugins
```

## Gotchas

- Some MCP servers (10X Genomics txg-mcp, ToolUniverse) require a separate binary download and are not bundled
- Skills are Apache 2.0, but MCP servers are third-party — check each provider's own terms before use
- Run the bundled /start command first to see which tools are actually connected and available
- Benchling and several connectors are placeholders that must be wired up before genomics/lab workflows work
- The plugin targets preclinical, early-stage R&D; it is not a substitute for validated clinical analysis

---
Generated by SkillMake from https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research on 2026-07-02T18:42:03.623Z.
Verify against source before relying on details.

File: ~/.claude/skills/knowledge-work-bio-research/SKILL.md