ClawBio@ClawBio

Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.

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

Queries and displays Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy, with an offline demo mode using synthetic biology data.

Generates a personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) by interrogating nutritionally-relevant SNPs and producing actionable dietary guidance, all computed locally.

Transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Scores a 224x224 tile and returns per-gene log1p-CPM values for any HGNC symbols you ask for, with a CSV, a report and a reproducibility bundle.

Takes raw whole-genome sequencing FASTQ files or a pre-existing VCF through variant calling, quality control, and polygenic risk score computation using the PGS Catalog.

Search scientific papers via the BGPT MCP server and retrieve structured experimental data — methods, results, conclusions, quality scores, and 25+ metadata fields per paper.

Computes phylogenetic distance matrices and trees from genomic VCF or FASTA data using the fastreeR hybrid Java/Python toolkit.

Authenticate, browse pipelines, samples, and projects, upload data, launch pipeline executions, and check run status on any Flow.bio instance via CLI.

Calculate polygenic risk scores from direct-to-consumer genetic data using published scoring files from the PGS Catalog and contextualize results against population reference distributions.

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

Automates sequencing quality control by running FastQC and MultiQC, extracting quality metrics, and generating publication-ready visualizations via a CLI or MCP stdio server.

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.

Performs differential expression analysis on bulk RNA-seq or pseudo-bulk count matrices with QC, PCA, and contrast testing.

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.

Takes pre-computed differential expression results from DESeq2, edgeR, limma, or PyDESeq2 and produces a structured, publication-ready summary with ranked gene lists, biological themes, and key observations.

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.

Identifies a medication from a photo and generates a genotype-informed dosage card using CPIC guidelines and real 23andMe data.

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

Performs HLA allele genotyping from WGS/WES VCF data, producing a structured markdown report and machine-readable JSON results.

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

Perform fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames via the polars-bio library, serving as a scalable alternative to bioframe and bedtools.

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

Predicts enhancer activity in DNA sequences using the hosted Genomic Intelligence G0 DeepSTARR model, returning per-window activity scores.

Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning.

Detect promoter regions in DNA sequences by calling the Genomic Intelligence G0 transformer (GENA-LM BERT Large) hosted API. Returns per-window promoter probabilities and called regions as a report and JSON, from a single FASTA input.

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

Queries 9 genomic databases in parallel for a given rsID, returning unified GWAS, PheWAS, eQTL, and fine-mapping reports.

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

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.

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

Scores genetic compatibility between all male-female pairings in a Genomebook generation, ranking optimal mating pairs based on heterozygosity, trait complementarity, and disease risk.

Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle.

Predicts chromatin state across 919 tracks (histone marks, DNase, TF binding) for DNA sequences via the hosted Genomic Intelligence API, producing a report and JSON results.

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.

Computes evidence-aware polygenic risk scores from local VCF or WGS files using the just-prs engine and a pinned local MCP server, with honest interpretation and model comparison.

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

Search, browse, and retrieve scientific protocols from protocols.io via REST API, including private protocols with client token authentication.

Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Gene-set pathway enrichment analysis using Enrichr — queries KEGG, GO (BP/MF/CC), Reactome, WikiPathways, MSigDB, and Disease Ontology. Produces ranked pathway tables, interactive bubble charts, and a reproducible Markdown report.

Runs NGS read QC, alignment, and BAM processing, wrapping FastQC, BWA/Bowtie2/Minimap2, SAMtools, and MultiQC for automated read-to-BAM workflows.

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

Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.

Compute organ-specific biological age from Olink proteomic data using Goeminne et al. (2025) elastic net aging clocks.

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

Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers

Discovers and executes bioinformatics tools from the Galaxy ecosystem via natural language, with multi-signal scoring, workflow templates, and reproducibility bundles.

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.

Predicts gene and transcript structure from a DNA sequence using the hosted Genomic Intelligence API, producing a report and JSON output.

Ancestry decomposition PCA against the Simons Genome Diversity Project

Predicts tissue or cell-type gene expression (log TPM and TPM) from a TSS-centered DNA sequence using the hosted Genomic Intelligence G0 Expression model, conditioned on a free-text cell-type description.

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

Automates genome-wide association studies from genotype files to publication-ready results, running PLINK2 QC and REGENIE regression with Manhattan and QQ plots.

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

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

Performs differential expression analysis on label-free quantitative (LFQ) proteomics data from MaxQuant and DIA-NN outputs, including preprocessing, imputation, statistical testing, and visualization.

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

Scaffolds a new ClawBio skill from a JSON/YAML spec or interactively, generating SKILL.md, Python skeleton, tests, and updating the catalog.