Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018),…
Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples.
Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers.
ISO 13485 Quality Management System specialist for medical device companies. Provides QMS implementation, maintenance, process optimization, and compliance expertise.
Four-phase debugging framework that ensures root cause identification before fixes. Use when encountering bugs, test failures, unexpected behavior, or when previous fix attempts…
When the user wants to create X (Twitter) post copy, threads, or optimize for X platform. Also use when the user mentions "X post," "X thread," "Twitter post," "Twitter t — from…
Creates unique, production-grade frontend interfaces with exceptional design quality. Use when user asks to build web components, pages, materials, posters, or applications (e.g.,…
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell a — from…
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution — from…
Documentation generation workflow covering API docs, architecture docs, README files, code comments, and technical writing. — from bg-szy/TOP-SKILLS
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing.
Execute Python code in a safe sandboxed environment via [inference.sh](https://inference.sh). Pre-installed: NumPy, Pandas, Matplotlib, requests, BeautifulSoup, Selenium — from…
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensio — from…
Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential…
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or — from…
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications.
Unified content extraction and action planning. Use when user says "learn-this <URL>", "learn this <URL>", "weave <URL>", "help me plan <URL>", "extract and plan <URL>" — from…
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructi — from…
Implement Command Query Responsibility Segregation for scalable architectures. Use when separating read and write models, optimizing query performance, or building event- — from…
Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing…
Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA.
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks…
Create AI-powered social media content for TikTok, Instagram, YouTube, Twitter/X. Generate: images, videos, reels, shorts, thumbnails, captions, hashtags.
Detects circadian and ultradian rhythms in time-series omics data using CosinorPy cosinor models, MetaCycle (JTK_CYCLE, ARSER), and RAIN non-parametric tests.
Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.
Design RESTful and GraphQL APIs following best practices. Use when creating new APIs, refactoring existing endpoints, or documenting API specifications.
When the user wants to add, optimize, or audit social share buttons (share article to X, LinkedIn, Facebook, etc.).
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions…
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses.
Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms.
Transform GWAS signals into actionable drug targets and repurposing opportunities. Performs locus-to-gene mapping, target druggability assessment, existing drug identification,…
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.
When the user wants to add, optimize, or audit a top announcement bar or sticky banner. Also use when the user mentions "announcement bar," "top banner," "sticky bar," "promo…
Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database.
Python patterns for system reliability — background jobs and task queues (Celery, async), resilience and recovery (retries, backoff, timeouts, circuit breakers via tenacity), and…
Use when creating or developing anything, before writing code or implementation plans - refines rough ideas into fully-formed designs through structured Socratic questioning,…
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms.
Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS.
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for m — from…
Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation.
Predict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition.
Integrate Firebase AI Logic (Gemini in Firebase) for intelligent app features. Use when adding AI capabilities to Firebase apps, implementing generative AI features, or setting up…
Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046),…
Extract content from specific URLs using Tavily's extraction API. Returns clean markdown/text from web pages.
Guides creation of effective Agent Skills with proper structure and validation. Use when users want to create a new skill, update an existing skill, or need guidance on s — from…
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex re — from…
Comprehensive guide for this Neovim configuration - a modular, performance-optimized Lua-based IDE. Use when configuring plugins, adding keybindings, setting up LSP servers,…
Biomedical OS Core & MCP Server
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude's capabilities with — from…
React and Next.js performance optimization guidelines from Vercel Engineering. This skill should be used when writing, reviewing, or refactoring React/Next.js code to ens — from…
Manage Power BI table partitions, named expressions (M/Power Query data sources), and calendar table configuration using pbi-cli.
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources.
This skill should be used when the user asks to "diagnose context problems", "fix lost-in-middle issues", "debug agent failures", "understand context poisoning", or mentions…
Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding…
Toolkit for creating animated GIFs optimized for Slack, with validators for size constraints and composable animation primitives.
This skill should be used when the user asks about "key startup metrics", "SaaS metrics", "CAC and LTV", "unit economics", "burn multiple", "rule of 40", "marketplace metrics", or…
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with — from…
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity…
This skill should be used when the user asks to "evaluate agent performance", "build test framework", "measure agent quality", "create evaluation rubrics", or mentions…