ClawBio

Query TCGA tumor biology through the ucscxenatoolspy API. Supports tumor-vs-normal differential expression, gene-gene correlation, survival association, and cancer catalogue browsing across 30+ TCGA cancer types.

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

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

Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.

Fetch a regional slice of plasma pQTL summary statistics from the UK Biobank Pharma Proteomics Project (UKB-PPP; Sun 2023 Nature) for a specific (protein, ancestry) measurement. Use when an agent needs per-variant beta / SE / p-value around a coloc-lead variant for downstream colocalisation, Mendelian randomisation, or regional plotting against a pQTL exposure. The canonical use case is the cis-window around the protein's coding gene TSS, but UKB-PPP releases full-genome summary stats per protein so any GRCh38 window (including trans loci) is supported when the user supplies an explicit (chromosome, start_bp, end_bp). Input: protein_label (HGNC or UniProt), ancestry, chromosome, start_bp, end_bp. Output: harmonised TSV slice + manifest + human-readable report.

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

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

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

Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json

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

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

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

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

Count rare, high-impact loss-of-function variants carried in a VCF, annotated with molecular consequence and population allele frequency

Blood RNA-seq expression-outlier detection for rare-disease diagnostics. Cases scored against a control reference panel; outliers ranked and filtered by a haploinsufficient disease-gene panel.

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

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

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 polars-bio. A scalable bioframe/bedtools alternative.

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

Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient). Agent- and demo-friendly.

Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.

ClawBio wrapper around nf-core/sarek 3.8.1 covering mapping through annotation for germline, tumor-only, and somatic paired analyses.

Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.

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

Two-sample Mendelian Randomisation from GWAS summary statistics with IVW, MR-Egger, weighted median/mode, and full sensitivity analysis (Cochran Q, Egger intercept, Steiger, F-statistic, leave-one-out).