Plugin Claude Code
Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D.
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MCP server "pubmed" as configured in openyak/openyak. Launched with uvx,pubmed-mcp.
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BioRender's hosted server: lets the agent create and edit scientific figures and diagrams in BioRender. Remote server at mcp.services.biorender.com.
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Anthropic's hosted bioRxiv/medRxiv server: lets the agent search and read life-science preprints. Remote server at mcp.deepsense.ai.
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Anthropic's hosted ClinicalTrials.gov server: lets the agent search registered clinical trials and read their status, conditions and interventions. Remote server at mcp.deepsense.ai.
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Anthropic's hosted ChEMBL server: lets the agent look up bioactive molecules, targets and assay data. Remote server at mcp.deepsense.ai.
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Sage Bionetworks' Synapse server: lets the agent find and read datasets, files and projects on the Synapse research data platform. Remote server at mcp.synapse.org.
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Wiley Scholar Gateway: lets the agent search and read Wiley's scholarly journals and books. Remote server at connector.scholargateway.ai.
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Owkin's hosted server: lets the agent query Owkin's biomedical and multi-omics knowledge. Remote server at mcp.k.owkin.com.
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Open Targets' hosted server: lets the agent query target–disease associations, drugs and genetics evidence. Remote server at mcp.platform.opentargets.org.
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Benchling's MCP server: lets the agent read and update entities, entries and results in a Benchling R&D workspace.
Skill Claude CodeCodex
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
Skill Claude CodeCodex
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis…
Skill Claude CodeCodex
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate…
Skill Claude CodeCodex
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics…
Skill Claude CodeCodex
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
Skill Claude CodeCodex
Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills before starting a new project.
Plugin Claude Code
Create, customize, and manage plugins tailored to your organization's tools and workflows. Configure MCP servers, adjust plugin behavior, and adapt templates to match how your team works.
Skill Claude CodeCodex
Customize a Claude Code plugin for a specific organization's tools and workflows. Use when: customize plugin, set up plugin, configure plugin, tailor plugin, adjust plugin settings, customize plugin connectors, customize plugin skill, tweak plugin, modify plugin configuration.
Skill Claude CodeCodex
Guide users through creating a new plugin from scratch in a cowork session. Use when users want to create a plugin, build a plugin, make a new plugin, develop a plugin, scaffold a plugin, start a plugin from scratch, or design a plugin. This skill requires Cowork mode with access to the outputs directory for…
Plugin Claude Code
Triage tickets, draft responses, escalate issues, and build your knowledge base. Research customer context and turn resolved issues into self-service content.
Skill Claude CodeCodex
Package an escalation for engineering, product, or leadership with full context. Use when a bug needs engineering attention beyond normal support, multiple customers report the same issue, a customer is threatening to churn, or an issue has sat unresolved past its SLA.
Skill Claude CodeCodex
Multi-source research on a customer question or topic with source attribution. Use when a customer asks something you need to look up, investigating whether a bug has been reported before, checking what was previously told to a specific account, or gathering background before drafting a response.
Skill Claude CodeCodex
Draft a professional customer-facing response tailored to the situation and relationship. Use when answering a product question, responding to an escalation or outage, delivering bad news like a delay or won't-fix, declining a feature request, or replying to a billing issue.