ClawBio
- 84 skills
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- 11 hours ago last updated
- ▌ Dnasp · clawbio bundleFull 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 multi-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 FASTA or NEXUS input; outputs DnaSP-compatible TSV and a Markdown report.
- ▌ Wgs Prs · clawbio bundleEnd-to-end WGS to polygenic risk score pipeline. Takes paired-end FASTQ files (or a pre-existing VCF) through nf-core/sarek for variant calling, applies VCF QC (normalisation, hard filtering, Ti/Tv and Het/Hom checks), then computes polygenic risk scores via the PGS Catalog. Fills the FASTQ to VCF gap upstream of the gwas-prs skill.
- ▌ Claw Amplicon Qc · clawbio bundle16S/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.
- ▌ Affinity Proteomics · clawbio bundleUnified 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.
- ▌ Cnv Acmg Classifier · clawbio bundleClassify 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.
- ▌ Rare Disease Rnaseq · clawbio bundleBlood 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.
- ▌ Organ Aging Studio · clawbio bundleInteractive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient). Agent- and demo-friendly.
- ▌ Claw Ancestry Pca · clawbio bundleAncestry decomposition PCA against the Simons Genome Diversity Project
- ▌ Claw Metagenomics · clawbio bundleShotgun metagenomics profiling — taxonomy, resistome, and functional pathways
- ▌ Deepspot M · clawbio bundleTranscriptome-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.
- ▌ Celltype Specificity Profiler · clawbio bundleGiven 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.
- ▌ Clinical Variant Prioritizer · clawbio bundleScreen 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).
- ▌ Eqtl Catalogue Region Fetch · clawbio bundleFetch 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.
- ▌ Locuscompare Region Render · clawbio bundleRender 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.
- ▌ Clinical Variant Reporter · clawbio bundleClassify 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.
- ▌ Gwas Catalog Region Fetch · clawbio bundleFetch 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.
- ▌ Rare High Impact Variants · clawbio bundleCount rare, high-impact loss-of-function variants carried in a VCF, annotated with molecular consequence and population allele frequency
- ▌ Drug Repurposing Screen · clawbio bundleObjective-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.
- ▌ Ld 1000g Region Compute · clawbio bundleCompute 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.
- ▌ Marker Dominance Mapper · clawbio bundleDeterministic marker-dominance region mapping from local spot-count CSVs
- ▌ Mendelian Randomisation · clawbio bundleTwo-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).
- ▌ Nfcore Scrnaseq Wrapper · clawbio bundleWrapper 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.
- ▌ Clawpathy Autoresearch · clawbio bundleEval-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.
- ▌ Wes Clinical Report En · clawbio bundleGenerates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.
- ▌ Wes Clinical Report Es · clawbio bundleGenerates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation, pharmacogenomic alerts, and follow-up recommendations.
- ▌ Ancestry Risk Profiler · clawbio bundleInfers 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.
- ▌ Claw Methylation Cycle · clawbio bundleMethylation cycle analysis — enzymatic activity profiles, Net Methylation Capacity, BH4 axis estimates, compound heterozygosity detection from SNP genotype data.
- ▌ Archaic Introgression · clawbio bundleDetect Neanderthal and Denisovan introgression segments from modern human genomes
- ▌ Nfcore Rnaseq Wrapper · clawbio bundleWrapper 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.
- ▌ Phylogenetics Builder · clawbio bundleEnd-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.
- ▌ Article Data Fetcher · clawbio bundleGiven 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.
- ▌ Crispr Screen Triage · clawbio bundleDeterministic CRISPR screen hit ranking from local guide-level count tables
- ▌ Nfcore Sarek Wrapper · clawbio bundleClawBio wrapper around nf-core/sarek 3.8.1 covering mapping through annotation for germline, tumor-only, and somatic paired analyses.
- ▌ Ukb Ppp Region Fetch · clawbio bundleFetch 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.
- ▌ Xena Tcga Gene Query · clawbio bundleQuery 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.
- ▌ Multiqc Reporter · clawbio bundleAggregates 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.
- ▌ Pathway Enricher · clawbio bundleGene-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.
- ▌ Proteomics Clock · clawbio bundleCompute organ-specific biological age from Olink proteomic data using Goeminne et al. (2025) elastic net aging clocks.
- ▌ Sample Qc Triage · clawbio bundleDeterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers
- ▌ Bigquery Public · clawbio bundleRun read-only SQL against BigQuery public datasets with local result capture, cost safeguards, and reproducibility outputs.
- ▌ Cell Detection · clawbio bundleCell 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.
- ▌ Turingdb Graph · clawbio bundleBuild, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning.
- ▌ Omics Target Evidence Mapper · clawbioAggregate public target-level evidence across omics and translational sources for research triage.
- ▌ Target Validation Scorer · clawbioEvidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns
- ▌ Bioconductor Bridge · clawbioBioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.
- ▌ Clinical Trial Finder · clawbioFind clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output
- ▌ Genome Match · clawbioScore genetic compatibility across all male-female pairings in a Genomebook generation
- ▌ Protocols Io · clawbioSearch, 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.
- ▌ Recombinator · clawbioProduce offspring genomes from parent pairs via meiotic recombination, mutation, and clinical evaluation
- ▌ Seq Wrangler · clawbioSequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
- ▌ Equity Scorer · clawbioCompute 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 · clawbioGalaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions
- ▌ Proteomics De · clawbioDifferential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output. Workflow includes preprocessing, imputation, and statistical testing.
- ▌ Ukb Navigator · clawbioSemantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.
- ▌ Vcf Annotator · clawbioAnnotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
- ▌ Data Extractor · clawbioExtract 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.
- ▌ Genome Compare · clawbioCompare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
- ▌ Profile Report · clawbioUnified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
- ▌ Repro Enforcer · clawbioExport any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
- ▌ Diff Visualizer · clawbioRich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast outputs.
- ▌ Illumina Bridge · clawbioImport DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
- ▌ Lit Synthesizer · clawbioSearch PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.
- ▌ Nutrigx Advisor · clawbioPersonalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.
- ▌ Scrna Embedding · clawbioLocal 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.
- ▌ Bio Orchestrator · clawbioMeta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
- ▌ Pharmgx Reporter · clawbioPharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
- ▌ Struct Predictor · clawbioLocal protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.
- ▌ Claw Semantic Sim · clawbioSemantic Similarity Index for disease research literature using PubMedBERT embeddings
- ▌ Methylation Clock · clawbioCompute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
- ▌ Pubmed Summariser · clawbioSearch PubMed for a gene name or disease term and generate a structured research briefing of the top recent English-language papers.
- ▌ Scrna Orchestrator · clawbioLocal 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.
- ▌ Variant Annotation · clawbioAnnotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
- ▌ Rnaseq De · clawbioDifferential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
- ▌ Drug Photo · clawbioMedication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance
- ▌ Gwas Lookup · clawbioFederated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.
- ▌ Gi Annotation · clawbio bundlePredicts gene and transcript structure from a DNA sequence using the hosted Genomic Intelligence API, producing a report and JSON output.
- ▌ Gi Expression · clawbio bundlePredicts 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.
- ▌ Skill Builder · clawbio bundleScaffolds a new ClawBio skill from a JSON/YAML spec or interactively, generating SKILL.md, Python skeleton, tests, and updating the catalog.
- ▌ Gi Enhancer · clawbio bundlePredicts enhancer activity in DNA sequences using the hosted Genomic Intelligence G0 DeepSTARR model, returning per-window activity scores.
- ▌ Gi Chromatin · clawbio bundlePredicts 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.
- ▌ Nutrigx · clawbio bundleGenerates a personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) by interrogating nutritionally-relevant SNPs and producing actionable dietary guidance, all computed locally.
- ▌ Gwas Prs · clawbio bundleCalculate polygenic risk scores from direct-to-consumer genetic data using published scoring files from the PGS Catalog and contextualize results against population reference distributions.
- ▌ Gi Splice · clawbio bundleDetect 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.
- ▌ Gi Promoter · clawbio bundleDetect 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.