synapse

Life Sciences Marketplace for Claude Code

This marketplace provides MCP (Model Context Protocol) servers and skills for life sciences tools. Install these plugins to access specialized research and analysis tools directly within Claude Code.

What's included:

• MCP Servers: Connect to external services like PubMed, BioRender, Synapse, and more
• Skills: Domain-specific workflows and analysis capabilities that extend Claude's expertise

Quick Start

# Add the marketplace
/plugin marketplace add anthropics/life-sciences

# Install MCP servers
/plugin install pubmed@life-sciences
/plugin install biorender@life-sciences
/plugin install synapse@life-sciences
/plugin install wiley-scholar-gateway@life-sciences
/plugin install 10x-genomics@life-sciences

# Install skills
/plugin install single-cell-rna-qc@life-sciences
/plugin install instrument-data-to-allotrope@life-sciences
/plugin install nextflow-development@life-sciences
/plugin install scvi-tools@life-sciences

For servers requiring authentication (all except PubMed), configure credentials after installation:

1. Type /plugin in Claude Code
2. Select "Manage plugins"
3. Find your installed server
4. Select "Configure"
5. Enter required credentials
6. Restart Claude Code

Available Plugins

Remote MCP Servers

PubMed

Plugin ID: pubmed@life-sciences

Search and access biomedical literature and research articles from PubMed.

Requirements: None - accessible to all users

BioRender

Plugin ID: biorender@life-sciences

Create and access scientific illustrations and diagrams.

Requirements: Free BioRender account (https://www.biorender.com)

Synapse.org

Plugin ID: synapse@life-sciences

Collaborative research data management platform by Sage Bionetworks.

Requirements: Free Synapse account (https://www.synapse.org)

Scholar Gateway (Wiley)

Plugin ID: wiley-scholar-gateway@life-sciences

Access academic research and publications from Wiley's Scholar Gateway.

Requirements: Free Scholar Gateway account

Local MCP Servers (MCPB)

10x Genomics Cloud

Plugin ID: 10x-genomics@life-sciences

Access 10x Genomics Cloud analysis data and workflows.

Requirements:

• 10x Genomics Cloud account (https://www.10xgenomics.com/products/cloud-analysis)
• Access token (generate from: https://cloud.10xgenomics.com/account/security)
• Note: Only useful if you have analysis data in your account

Skills

Single-Cell RNA-seq Quality Control

Plugin ID: single-cell-rna-qc@life-sciences

Automated quality control workflow for single-cell RNA-seq data following scverse best practices. Performs MAD-based filtering with comprehensive visualizations.

Instrument Data to Allotrope

Plugin ID: instrument-data-to-allotrope@life-sciences

Convert instrument data to Allotrope Simple Model (ASM) format for standardized data exchange and analysis.

Nextflow Development

Plugin ID: nextflow-development@life-sciences

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on local or public GEO/SRA sequencing data. Designed for bench scientists who need to run large-scale omics analyses without specialized bioinformatics training.

Supported pipelines:

• rnaseq: Gene expression and differential expression analysis
• sarek: Germline and somatic variant calling (WGS/WES)
• atacseq: Chromatin accessibility analysis

Features:

• Download public datasets from GEO/SRA
• Auto-detect data types and suggest appropriate pipelines
• Generate pipeline-compatible samplesheets
• Environment validation and troubleshooting guidance

Requirements: Docker and Nextflow installed locally

scvi-tools

Plugin ID: scvi-tools@life-sciences

Deep learning toolkit for single-cell omics analysis using scvi-tools. Includes model selection guidance, training workflows, and integration pipelines for scVI, scANVI, totalVI, PeakVI, MultiVI, and more.

Detailed Installation

1. Add the marketplace (one time)

/plugin marketplace add https://github.com/anthropics/life-sciences.git

2. Install specific plugins

# Remote MCP servers (no configuration needed for PubMed)
/plugin install pubmed@life-sciences
/plugin install biorender@life-sciences
/plugin install synapse@life-sciences
/plugin install wiley-scholar-gateway@life-sciences

# Local MCP servers (require configuration)
/plugin install 10x-genomics@life-sciences

# Skills (no configuration needed)
/plugin install single-cell-rna-qc@life-sciences
/plugin install instrument-data-to-allotrope@life-sciences
/plugin install nextflow-development@life-sciences
/plugin install scvi-tools@life-sciences

3. Configure credentials (if needed)

For servers requiring authentication, use the /plugin menu:

1. Type /plugin in Claude Code
2. Select "Manage plugins"
3. Find your installed server
4. Select "Configure" (if available)
5. Enter your API credentials