clawbio

Run a ClawBio bioinformatics analysis on user-provided genetic data

List all available ClawBio bioinformatics skills with their status and capabilities

Build a new ClawBio skill from the official template with full conformance enforcement.

Run a ClawBio skill demo with built-in sample data

Run read-only SQL against BigQuery public datasets with local result capture, cost safeguards, and reproducibility outputs.

Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.

Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.

Cell segmentation in fluorescence microscopy images. Supports Cellpose/cpsam (Cellpose 4.0) with additional backends planned. Produces segmentation masks, per-cell morphology metrics (area, diameter, centroid, eccentricity), overlay figures, and a report.md.

Place your study cohort in global genetic context by computing a joint PCA against the Simons Genome Diversity Project (SGDP) — 345 samples from 164 populations spanning every inhabited continent.

Comprehensive shotgun metagenomics analysis combining taxonomic classification, antimicrobial resistance gene detection, and functional pathway profiling from paired-end FASTQ files.

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Find clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output

Classify germline variants from VCF/BCF files according to the ACMG/AMP 2015 28-criteria evidence framework and generate clinical-grade interpretation reports with per-variant evidence audit trails and ACMG SF v3.2 secondary findings screening.

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels

Extract numerical data from scientific figure images using Claude vision + OpenCV calibration. Supports 26+ plot types including bar charts, scatter plots, forest plots, Kaplan-Meier curves, box plots, and more.

Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast outputs.

Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance

Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.

Statistical fine-mapping of GWAS loci using SuSiE, SuSiE-inf, and Approximate Bayes Factors to identify credible sets and posterior inclusion probabilities (PIPs) for causal variant discovery. SuSiE-inf adds an infinitesimal polygenic component for improved calibration at well-powered loci.

Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

Score genetic compatibility across all male-female pairings in a Genomebook generation

Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.

Calculate polygenic risk scores from DTC genetic data using the PGS Catalog

Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.

Query and display Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy. Supports offline demo mode with synthetic biology data.

Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.

Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.

Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.

Aggregate public target-level evidence across omics and translational sources for research triage.

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.

Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output. Workflow includes preprocessing, imputation, and statistical testing.

Search, browse, and retrieve scientific protocols from protocols.io via REST API. Client token authentication for private protocols. Use when user mentions protocols.io, lab protocols, DOI lookup, protocol search, protocol steps, or scientific methods.

Search PubMed for a gene name or disease term and generate a structured research briefing of the top recent English-language papers.

Produce offspring genomes from parent pairs via meiotic recombination, mutation, and clinical evaluation

Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.

Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.

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.

Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.

Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mapping

Protein structure prediction with Boltz-2. Accepts YAML inputs (single protein or multi-chain complex), runs boltz predict, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.

Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns

Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.

Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.

Generates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation, pharmacogenomic alerts, and follow-up recommendations.