ClawBio@ClawBio

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

Searches UK Biobank's 12,000+ data fields and publications by natural language query, returning ranked field IDs and descriptions for research questions.

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.

Annotates VCF variants using Ensembl VEP, ClinVar, and gnomAD, ranks them by predicted impact, and generates a reproducible report.

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

Assesses genome, transcriptome, and protein completeness with BUSCO v6, automatically resolving the correct lineage from an organism description and generating reproducible reports.

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.

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

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.

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.

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.

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

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

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.

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.

Detect Neanderthal and Denisovan introgression segments from modern human genomes

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

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.

End-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.

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.

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

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.

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.

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.

Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified. Use when an agent needs LD coloring for a regional plot or LD pruning around a candidate causal variant. Single client (on-demand region fetch from EBI 1000G FTP); no multi-GB cold-start.

Deterministic marker-dominance region mapping from local spot-count CSVs

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).

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.

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

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.

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.

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

Render a 4-panel regional LocusCompare diagnostic for one (lead variant, exposure study, outcome study) tuple - overlays GWAS Manhattan, QTL Manhattan, GENCODE gene track, and cross-trait scatter colored by LD r². Use when an agent needs visual confirmation that two GWAS / QTL signals share the same causal variant (the Liu 2019 LocusCompare convention). Inputs: lead variant + two pre-fetched harmonised sumstats slices (or eQTL Catalogue / GWAS Catalog identifiers for bundled fetch). Output: PNG + JSON manifest.

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.

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).

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

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.