bio-research

Plugin bio-research from marketplace knowledge-work-plugins in sun2443/designer-skills. Commands read from the repo's manifest — 1 month ago.

Skills (6)

• instrument-data-to-allotrope

  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. Out

• 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 r

• scientific-problem-selection

  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

• scvi-tools

  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 t

• 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 si

• 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.

MCP servers (10)

• pubmed

  connects to: https://pubmed.mcp.claude.com/mcp

• biorender

  connects to: https://mcp.services.biorender.com/mcp

• biorxiv

  connects to: https://mcp.deepsense.ai/biorxiv/mcp

• c-trials

  connects to: https://mcp.deepsense.ai/clinical_trials/mcp

• chembl

  connects to: https://mcp.deepsense.ai/chembl/mcp

• synapse

  connects to: https://mcp.synapse.org/mcp

• wiley

  connects to: https://connector.scholargateway.ai/mcp

• owkin

  connects to: https://mcp.k.owkin.com/mcp

• ot

  connects to: https://mcp.platform.opentargets.org/mcp

• benchling