Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional dataset-level plus within-cluster contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
Record the outcome of applying an evolution strategy. Use after resolving an error where prismer-evolve-analyze provided a recommendation, to feed back success or failure to the network.
Expert in vector databases, embedding strategies, and semantic search implementation. Masters Pinecone, Weaviate, Qdrant, Milvus, and pgvector for RAG applications, recommendation systems, and similar
Multi-agent coordination patterns for OpenCode swarm workflows. Use when work benefits from parallelization or coordination. Covers: decomposition, worker spawning, file reservations, progress tracking, and review loops.
Multi-agent coordination patterns for OpenCode swarm workflows. Use when work benefits from parallelization or coordination. Covers: decomposition, worker spawning, file reservations, progress tracking, and review loops.
Query the KEGG REST API for metabolic pathways, genes, compounds, drugs, and diseases. Use when the user needs pathway mapping, gene-to-pathway links, compound info, or cross-reference ID conversion. NOT for protein sequences (use UniProt), 3D structures (use PDB), or variant/SNP data (use NCBI).
Analyzes protein 3D structures, performs homology modeling, interprets AlphaFold predictions, conducts molecular docking, and evaluates protein-ligand interactions; trigger when users ask about PDB files, folding, binding sites, or structural biology.
Query the UniProt REST API for protein sequences, function annotations, structure info, and cross-references. Use when the user needs protein data, gene-to-protein mapping, functional annotation, or FASTA sequences. NOT for nucleotide sequences (use NCBI), 3D structure files (use PDB), or pathway data (use KEGG).
Single-cell RNA-seq analysis with scanpy and anndata. Use when: (1) scRNA-seq preprocessing and QC, (2) clustering and cell type annotation, (3) differential expression analysis, (4) trajectory and pseudotime analysis, (5) UMAP/tSNE visualization. NOT for: bulk RNA-seq differential expression (use DESeq2/edgeR), protein structure analysis (use pdb-structure), or imaging data.
Query the RCSB PDB API for protein 3D structures, experimental metadata, and structure files. Use when the user needs crystal or cryo-EM structure data, PDB entries, resolution info, or structure file downloads. NOT for protein sequences/annotations (use UniProt), gene data (use NCBI), or pathway info (use KEGG).
"Query the Open Targets Platform GraphQL API for gene-drug-disease associations, evidence scores, and therapeutic target validation. Use when the user needs disease associations for a gene, drug evidence for a target, or target prioritization for a disease. NOT for compound property lookup (use pubchem-compound), NOT for bioactivity measurements (use chembl-drug), NOT for protein 3D structures (use pdb-structure)."
Query NCBI E-utilities for GenBank sequences, gene info, SNPs, ClinVar variants, and literature links. Use when the user needs nucleotide/protein sequences from GenBank, gene summaries, variant data, or cross-database links. NOT for protein annotations (use UniProt), 3D structures (use PDB), or pathway mapping (use KEGG).
Orchestrates a genomics analysis workflow from gene query through expression analysis to pathway enrichment. Use when investigating gene function, analyzing expression data, or performing pathway-level interpretation. NOT for pure protein structure modeling or drug-target interaction analysis.
Performs genomics analyses including gene expression profiling, BLAST sequence alignment, GWAS interpretation, variant calling, and genome assembly tasks; trigger when the user mentions DNA/RNA sequences, SNPs, gene panels, or comparative genomics.
"Bioinformatics operations via Biopython. Use when: user asks about DNA/protein sequences, BLAST, or PDB structures. NOT for: clinical genomics or variant calling pipelines."
