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SkillsMP a collecté 97 skills depuis ClawBio/ClawBio. Ouvrez un skill pour examiner sa source et ses détails.
Affichage de 40 skills collectés sur 97.
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.
Langue du texte source : anglais
Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.
Langue du texte source : anglais
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…
Langue du texte source : anglais
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.
Langue du texte source : anglais
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
Langue du texte source : anglais
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
Langue du texte source : anglais
Compute evidence-aware polygenic risk scores from a local VCF or WGS file through the validated just-prs engine and a pinned local just-prs MCP server.
Langue du texte source : anglais
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.
Langue du texte source : anglais
ClawBio wrapper around nf-core/sarek 3.8.1 covering mapping through annotation for germline, tumor-only, and somatic paired analyses.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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…
Langue du texte source : anglais
Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient). Agent- and demo-friendly.
Langue du texte source : anglais
Compute organ-specific biological age from Olink proteomic data using Goeminne et al. (2025) elastic net aging clocks.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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…
Langue du texte source : anglais
Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).
Langue du texte source : anglais
End-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.
Langue du texte source : anglais
Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
Langue du texte source : anglais
Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.
Langue du texte source : anglais
Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
Langue du texte source : anglais
Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
Langue du texte source : anglais
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.
Langue du texte source : anglais
Count rare, high-impact loss-of-function variants carried in a VCF, annotated with molecular consequence and population allele frequency
Langue du texte source : anglais
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…
Langue du texte source : anglais
Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
Langue du texte source : anglais
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
Langue du texte source : anglais
Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json
Langue du texte source : anglais
Methylation cycle analysis — enzymatic activity profiles, Net Methylation Capacity, BH4 axis estimates, compound heterozygosity detection from SNP genotype data.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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. Async-only — the pipeline takes ~20 s for ~20 kbp.
Langue du texte source : anglais
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.
Langue du texte source : anglais
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.
Langue du texte source : anglais
Predict tissue / cell-type expression (log TPM + TPM) from a 9,198 bp TSS-centered DNA sequence 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…
Langue du texte source : anglais
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.
Langue du texte source : anglais
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.
Langue du texte source : anglais
Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
Langue du texte source : anglais
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.
Langue du texte source : anglais
NGS read QC, alignment, and BAM processing pipeline. Wraps FastQC, BWA/Bowtie2/Minimap2, SAMtools, and MultiQC for automated read-to-BAM workflows.
Langue du texte source : anglais