clawbio

Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.

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.

Infers genetic super-population ancestry from a 23andMe/AncestryDNA file and computes ancestry-stratified odds ratios with an exploratory Ancestry Elevation Score (AES) showing where ancestry-specific GWAS effect sizes diverge from European reference estimates.

Detect Neanderthal and Denisovan introgression segments from modern human genomes

Given an article DOI or PubMed ID, discover and download the genomics data files deposited by the authors (VCF, FASTA, H5AD, CSV, JSON, BAM, etc.) from public repositories such as GEO, ENA, Zenodo, Figshare, Dryad, and OSF.

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

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.

Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation. Exposes an MCP stdio server for live AI integration alongside a ClawBio CLI runner.

Genome, transcriptome, and protein completeness assessment via BUSCO v6. Agentic lineage routing from organism description, all three BUSCO modes, auto-lineage support, and full demo mode without the BUSCO binary.

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.

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.

16S/18S rRNA amplicon preprocessing — from raw paired-end FASTQ files through N removal and primer trimming, producing outputs ready for DADA2 quality filtering and denoising. Deliberately stops before quality-filtering decisions that require researcher judgment.

Ancestry decomposition PCA against the Simons Genome Diversity Project

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

Methylation cycle analysis — enzymatic activity profiles, Net Methylation Capacity, BH4 axis estimates, compound heterozygosity detection from SNP genotype data.

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Eval-driven skill tuning. Given a task and an LLM-judge rubric, iteratively rewrites a SKILL.md until a downstream executor agent performs well against the judge. Low-code: all evaluation is LLM-as-judge, not deterministic Python.

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

Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance model and zygosity, following the pathogenicity-screening method of Corpas et al. 2021 (Whole Genome Interpretation for a Family of Five).

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

Classify structural variants / copy-number variants (deletions and duplications) using the ClinGen / ACMG 2019 (Riggs et al. 2020) point framework and return a five-tier classification with a per-section evidence trail. Germline CNV interpretation, not SNV/indel.

Deterministic CRISPR screen hit ranking from local guide-level count tables

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.

Summarise pre-computed differential expression results with ranked gene lists, biological themes, and publication-ready interpretation.

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.

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

Full reimplementation of DnaSP 6 for population genetics analysis of aligned DNA sequences. Covers nucleotide diversity, haplotype statistics, neutrality tests (Tajima's D, Fu & Li's D*/F*, R2), linkage disequilibrium (D, D', R², ZnS, Za, ZZ), minimum recombination (Rm), mismatch distribution, InDel polymorphism, between-population divergence (Dxy, Da, fixed/shared sites), outgroup-based Fu & Li D/F tests (fuliout), the HKA two-locus neutrality test (hka), the McDonald-Kreitman test (mk), Ka/Ks (dN/dS) via the Nei-Gojobori (1986) method (kaks), Fu's Fs test (fufs), the site frequency spectrum (sfs, folded and outgroup-unfolded), transition/transversion ratio (tstv), and codon usage bias - RSCU (Sharp & Li 1987) and ENC (Wright 1990) (codon). Accepts pre-aligned FASTA/NEXUS or a multi-sample VCF (one MSA per CHROM); outputs DnaSP-compatible TSV and a Markdown report.

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

Objective-driven pooled viability screen analysis: QC, hit calling, context-selectivity, biomarker sweep, and ranked repurposing candidates. Format-agnostic via schema.yaml + objective.yaml; includes offline demo.

Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset (study × tissue × quantification method). Input: dataset_id, chromosome, start, end, optional molecular_trait_id. Output: harmonised TSV slice.

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.

Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).

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.

Flow.bio API bridge — authenticate, browse pipelines/samples/projects, search, upload data, launch pipeline executions, and check run status on any Flow instance.

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

Predict gene and transcript structure (intervals, exons, strand) from a DNA sequence using the Genomic Intelligence DNA Annotation model, via the hosted /v1/tasks/annotation/predict API. Submitted asynchronously — the pipeline takes ~20 s for ~20 kbp.

Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.

Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API. Returns per-window activity scores.

Predict tissue / cell-type expression (log TPM + TPM) from a 9,198–500,000 bp TSS-centered DNA sequence (longer than one 9,198 bp window needs --tss-index) using the Genomic Intelligence G0 Expression model, via the hosted /v1/tasks/expression/predict API. The model is conditioned on a free-text cell-type / assay description.

Detect promoter regions in DNA sequences using the Genomic Intelligence G0 transformer (GENA-LM BERT Large), via the hosted /v1/tasks/promoter/predict API. Returns per-window promoter probabilities and called regions.

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.

Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP. Use when an agent needs GWAS beta / SE / p-value for every variant in a window for one specific study (GCST accession). Input: accession, chromosome, start, end. Output: harmonised TSV slice in canonical format.

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

End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing. Produces Manhattan plots, QQ plots, clumped lead variants, and structured summary statistics.

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