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Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D.
written by ForgeCat
AI-powered research assistant for the life sciences. Connects Claude to 10 preclinical research databases and tools, and bundles 6 analysis skills covering single-cell genomics, bioinformatics pipelines, instrument data standardization, and scientific strategy.
ForgeCatnpx forgecat install @forgecat/anthropics_knowledge-work-plugins_bio-research
| Skill | Description |
|---|---|
start | 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. orientation |
single-cell-rna-qc | 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. single-cell |
scvi-tools | Deep learning for single-cell analysis using scvi-tools. Covers scVI/scANVI data integration and batch correction, ATAC-seq analysis with PeakVI, CITE-seq multi-modal analysis with totalVI, multiome RNA+ATAC with MultiVI, spatial transcriptomics deconvolution with DestVI, label transfer with scANVI/scArches, and RNA velocity with veloVI. deep-learning single-cell |
nextflow-development | 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, GSE/GSM/SRR accessions, or samplesheet creation. pipelines |
instrument-data-to-allotrope | Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Supports auto-detection of instrument types across 40+ categories including cell counters, spectrophotometers, plate readers, qPCR, and chromatography systems. data-standardization |
scientific-problem-selection | Systematic framework for research problem selection, project ideation, troubleshooting stuck projects, and strategic scientific decisions. Based on Fischbach & Walsh's framework. Covers ideation, risk assessment, optimization, decision trees, adversity planning, and integration synthesis. strategy |
| Server | Transport | URL | Category |
|---|---|---|---|
| PubMed | http | https://pubmed.mcp.claude.com/mcp | literature |
| bioRxiv/medRxiv | http | https://mcp.deepsense.ai/biorxiv/mcp | literature |
| Wiley Scholar Gateway | http | https://connector.scholargateway.ai/mcp | journal access |
| Synapse | http | https://mcp.synapse.org/mcp | data repository |
| ChEMBL | http | https://mcp.deepsense.ai/chembl/mcp | chemical database |
| Open Targets | http | https://mcp.platform.opentargets.org/mcp | drug targets |
| ClinicalTrials.gov | http | https://mcp.deepsense.ai/clinical_trials/mcp | clinical trials |
| BioRender | http | https://mcp.services.biorender.com/mcp | scientific illustration |
| Owkin | http | https://mcp.k.owkin.com/mcp | AI research |
| Benchling | http | (URL not yet configured) | lab platform |
| Field | Value |
|---|---|
| Author | Anthropic |
| Original repository | https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research |
| Version | 0.0.7 |
| Original commit | d2ba7f6 |
| License | Apache-2.0 |
| Source platform | Claude Code plugin (Cowork) |
| Platform | Status |
|---|---|
| Claude Code | Tested |
| Cursor | Partial |
| Codex | Tested |
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