This repository provides a marketplace for Claude Code, offering Model Context Protocol (MCP) servers and domain-specific skills tailored for life sciences research and analysis. It enables users to seamlessly integrate external data sources and analytical tools, such as PubMed, BioRender, and Nextflow pipelines, directly within the Claude Code environment, thereby accelerating research workflows and data interpretation.

How It Works

The marketplace functions by exposing external services and analytical capabilities as plugins within Claude Code. MCP servers act as connectors to third-party platforms (e.g., PubMed, Synapse), abstracting their APIs. Skills provide pre-packaged, domain-specific workflows, like single-cell RNA-seq quality control or running complex bioinformatics pipelines via Nextflow. This architecture allows users to query literature, generate figures, manage data, and execute omics analyses without leaving the Claude Code interface.

Quick Start & Requirements

• Add Marketplace: /plugin marketplace add https://github.com/anthropics/life-sciences.git
• Install Plugins: Use /plugin install <plugin_id>@life-sciences (e.g., pubmed@life-sciences, biorender@life-sciences, nextflow-development@life-sciences).
• Prerequisites:
  • PubMed: None.
  • BioRender, Synapse, Wiley Scholar Gateway: Free accounts required.
  • 10x Genomics Cloud: 10x Genomics Cloud account and access token.
  • Nextflow Development: Docker and Nextflow installed locally.
• Configuration: For authenticated servers, use the /plugin menu to manage and configure credentials. Restart Claude Code after installation and configuration.
• Links: BioRender (https://www.biorender.com), Synapse (https://www.synapse.org), 10x Genomics Cloud (https://www.10xgenomics.com/products/cloud-analysis).

Highlighted Details

• MCP Servers: Integrates with PubMed for literature search, BioRender for scientific illustrations, Synapse for collaborative data management, Wiley Scholar Gateway for academic publications, and 10x Genomics Cloud for analysis data.
• Skills: Includes automated single-cell RNA-seq QC (single-cell-rna-qc), data standardization to Allotrope Simple Model (instrument-data-to-allotrope), and a robust Nextflow development skill (nextflow-development) for running nf-core pipelines (rnaseq, sarek, atacseq) locally.
• scvi-tools Skill: Offers a deep learning toolkit for single-cell omics analysis, supporting various models like scVI, scANVI, and MultiVI.

Maintenance & Community

Support for the Claude Code plugin system is available via #claude-cli-feedback on Anthropic's Slack. Support for individual MCP servers should be directed to their respective providers. No other community channels or contributor information is detailed in the README.

Licensing & Compatibility

Individual MCP servers are licensed by their respective providers; users must consult each provider's terms of service. Compatibility for commercial use or closed-source linking is dependent on these individual licenses.

Limitations & Caveats

The Benchling plugin has been removed due to limitations with tenant-specific URLs. Authentication is required for most services, necessitating account creation and credential management. The nextflow-development skill requires local installations of Docker and Nextflow.