Container

ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.

ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.

Biology research tools reference. Always available inside agent containers.

Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS".

Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".

Mass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.

Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Triggers on "kegg", "pathway", "metabolic pathway", "signaling pathway", "pathway genes".

SEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and publication-quality PDF report generation via Typst templates. Triggers on "SEC", "size exclusion", "chromatography", "oligomer analysis", "protein assembly", "SEC report".

Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on "skills hub", "more skills", "install skill", "community skills", "find a skill for".

Customize your own agent — add capabilities, install packages, add MCP servers, edit code or CLAUDE.md. Use when the user asks you to add a feature, install a tool, or modify how you work. For non-trivial code changes, delegate to a builder agent via create_agent.

Run BLAST sequence similarity searches. Use when the user asks to BLAST a sequence, find similar sequences, identify a gene/protein, or do homology search. Triggers on "blast", "sequence similarity", "homology", "identify sequence".

Shotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.

Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".

Query Ensembl for genomic data. Use when user asks about gene coordinates, genomic sequences, variants, gene structure, exons, transcripts, or species comparison. Triggers on "ensembl", "gene coordinates", "genomic location", "exon", "transcript", "variant location", "rsid", "rs number".

Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".

Query InterPro for protein domains and families. Use when user asks about protein domains, functional sites, protein families, domain architecture, or motifs. Triggers on "interpro", "protein domain", "domain architecture", "protein family", "functional site", "motif".

Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".

Query STRING for protein-protein interactions. Use when user asks about protein interactions, interaction networks, binding partners, or interactome. Triggers on "string", "protein interaction", "interaction network", "binding partners", "interactome", "PPI".

Review SDS-PAGE or protein purification gel images using DNA sequence, protein sequence, base-pair length, expected protein size, and lane labels. Use when the user wants to judge whether a gel ran well, whether the main band matches the expected product, or whether there may be impurities, degradation, aggregation, or low expression.

Pro frontend engineering discipline. Enforces build-test-verify workflow for every web project. Never declare done until the site is built, tested, responsive, accessible, and visually verified in a real browser. Pairs with a deployment skill such as vercel-cli, where one is installed.

Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.

Query AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".

Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables, figure captions, callout boxes, and page headers/footers.

Query OpenTargets for drug targets, disease associations, and therapeutic evidence. Use when user asks about drug targets, disease mechanisms, target validation, or drug-disease associations. Triggers on "opentarget", "drug target", "target validation", "disease association", "therapeutic target", "drug for disease".

Analyze DNA/RNA/protein sequences. Use when the user provides a sequence and asks for analysis, translation, GC content, ORFs, motifs, restriction sites, or primer design. Triggers on "sequence", "translate", "GC content", "ORF", "primer", "restriction", "complement", "reverse complement".

Structure retrieval, confidence-aware AlphaFold DB usage, coordinate download, PAE and pLDDT interpretation, and structure-guided biological annotation.

Bulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE figures.

Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA models - no local GPU. Use when the user has a gene symbol, genomic region, or DNA/FASTA sequence and wants promoter, splice-site, enhancer, chromatin, expression (log TPM), or de-novo gene annotation predictions. Triggers on "genomic intelligence", "promoter prediction", "splice site", "enhancer activity", "chromatin state", "expression from sequence", "log TPM", "gene annotation", "DNA language model", "genomicintelligence.ai".

Standard scRNA-seq preprocessing and clustering with Scanpy. Use for QC, normalization, HVG selection, PCA, neighbor graph construction, UMAP, Leiden clustering, and export of an analysis-ready AnnData object.