> ClawBio/ClawBio
> bioconductor-bridge
Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.
> bio-orchestrator
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
> claw-ancestry-pca
--- name: claw-ancestry-pca version: 0.1.0 description: Ancestry decomposition PCA against the Simons Genome Diversity Project author: Manuel Corpas license: MIT tags: - population-genetics - PCA - ancestry - SGDP - global-diversity inputs: - name: vcf type: file format: [vcf, vcf.gz] description: VCF file with genotype data for your study cohort - name: pop-map type: file format: [tsv, txt] description: Tab-separated file mapping sample IDs to population la
> claw-metagenomics
--- name: claw-metagenomics version: 0.1.0 description: Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways author: Manuel Corpas license: MIT tags: - metagenomics - antimicrobial-resistance - taxonomy - functional-profiling - environmental - WHO-critical-ARGs inputs: - name: r1 type: file format: [fastq, fastq.gz, fq, fq.gz] description: Forward reads (paired-end FASTQ R1) - name: r2 type: file format: [fastq, fastq.gz, fq, fq.gz]
> claw-semantic-sim
Semantic Similarity Index for disease research literature using PubMedBERT embeddings
> clinical-trial-finder
Find clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output
> clinpgx
Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
> data-extractor
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.
> diff-visualizer
Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast outputs.
> drug-photo
Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance
> equity-scorer
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.
> galaxy-bridge
Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions
> genome-compare
Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
> gwas-lookup
Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.
> gwas-prs
Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
> illumina-bridge
Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
> labstep
Interact with the Labstep electronic lab notebook API using labstepPy. Query experiments, protocols, resources, inventory, and other lab entities.
> lit-synthesizer
Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.
> methylation-clock
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
> nutrigx-advisor
Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.
> omics-target-evidence-mapper
Aggregate public target-level evidence across omics and translational sources for research triage.
> pharmgx-reporter
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
> profile-report
Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
> proteomics-de
Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output. Workflow includes preprocessing, imputation, and statistical testing.
> protocols-io
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.
> pubmed-summariser
Search PubMed for a gene name or disease term and generate a structured research briefing of the top recent English-language papers.
> repro-enforcer
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
> rnaseq-de
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
> scrna-embedding
Local scVI-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.
> scrna-orchestrator
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 two-group contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
> seq-wrangler
Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
> struct-predictor
Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.
> target-validation-scorer
Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns
> ukb-navigator
Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.
> variant-annotation
Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
> vcf-annotator
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.