instrument-data-to-allotrope
🎯Skillfrom anthropics/life-sciences
|Converts raw scientific instrument data into standardized Allotrope Data Format (ADF) for improved data interoperability and archiving.
Installation
npx skills add https://github.com/anthropics/life-sciences --skill instrument-data-to-allotropeSkill Details
Overview
# 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
```bash
# 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:
- Type
/pluginin Claude Code - Select "Manage plugins"
- Find your installed server
- Select "Configure"
- Enter required credentials
- 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.
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