Use when starting feature work that needs isolation from current workspace or before executing implementation plans - creates isolated git worktrees with smart directory — from…
Build end-to-end MLOps pipelines from data preparation through model training, validation, and production deployment.
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation.
Extend or continue an existing video clip on RunComfy via the `runcomfy` CLI. Routes to Google Veo 3-1's `extend-video` and `fast/extend-video` endpoints — pick the sourc — from…
Update all documentation in .plans, CLAUDE.md files, docs, and .tasks to match current codebase state.
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
Use when completing tasks, implementing major features, or before merging to verify work meets requirements — from bg-szy/TOP-SKILLS
Robust workflow checkpoint and resume. Handles session interruption, state recovery, and safe resume across all workflow phases.
Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.
Build an insurance-grade home inventory from a folder of photos and receipts -- identifies items, pulls values from receipts, estimates replacement costs, organizes by room, and…
Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven,…
Modern React UI patterns for loading states, error handling, and data fetching. Use when building UI components, handling async data, or managing UI states.
Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies — from bg-szy/TOP-SKILLS
Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+.
Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database.
Vitest testing patterns and strategies for unit tests, agent tests, and API tests with Supabase mocking
Generate AI videos on RunComfy via the `runcomfy` CLI — a smart router across the full video-model catalog: HappyHorse 1.0 (Arena #1, native in-pass audio), Wan-AI Wan 2- — from…
Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC — from…
Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods.
Master Bash Automated Testing System (Bats) for comprehensive shell script testing. Use when writing tests for shell scripts, CI/CD pipelines, or requiring test-driven de — from…
Browser automation CLI for AI agents. Use for website interaction, form automation, screenshots, scraping, and web app verification.
Generate and edit images on RunComfy via the `runcomfy` CLI — a smart router across the full image-model catalog: FLUX 2 (Klein 9B/4B, Pro, Dev, Flash, Turbo, Max), Googl — from…
Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence score — from…
Generate images with Google Gemini native image models via inference.sh CLI. Models: Gemini 3 Pro Image, Gemini 2.5 Flash Image.
Shell script static analysis and linting. USE WHEN shellcheck, lint shell, bash lint, sh lint, script analysis, shell errors, SC codes, shell best practices.
Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework.
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water — from…
Use when completing tasks, implementing major features, or before merging to verify work meets requirements — from bg-szy/TOP-SKILLS
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.
Intelligently deploys Azure OpenAI models to optimal regions by analyzing capacity across all available regions.
Implement comprehensive evaluation strategies for LLM applications using automated metrics, human feedback, and benchmarking.
Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB. Use when choosing a format (mmCIF/PDBx vs legacy PDB vs BinaryCIF) for a structure that…
Generate AI videos with Google Veo, Seedance 2.0, HappyHorse, Wan, Grok and 40+ models via inference.sh CLI.
Token-efficient library documentation fetcher using Context7 MCP with 86.8% token savings through intelligent shell pipeline filtering.
Create distributable Python packages with proper project structure, setup.py/pyproject.toml, and publishing to PyPI.
Analyze API, schema, and contract changes; map affected consumers, assess business risk, generate an impact report, and support commit guarding with compatibility fixes.
Optimize vector index performance for latency, recall, and memory. Use when tuning HNSW parameters, selecting quantization strategies, or scaling vector search infrastruc — from…
Generate AI images with FLUX, Gemini, Grok, Seedream, Reve and 50+ models via inference.sh CLI. Models: FLUX Dev LoRA, FLUX.2 Klein LoRA, Gemini 3 Pro Image, Grok Imagine — from…
Azure FinOps reservation analysis, cost validation, waste discovery, and executive reporting. USE WHEN user says 'validate costs', 'check reservations', 'find waste', 'orphaned…
Use when preparing photos or images for a news wire, publication, photo CMS, or archive — embedding caption, byline, credit, alt text, keywords, copyright or Creative Commons…
Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods.
Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters — from…
Master Unity ECS (Entity Component System) with DOTS, Jobs, and Burst for high-performance game development.
When the user wants to create, optimize, or audit a careers or jobs page. Also use when the user mentions "careers," "jobs," "hiring," "open positions," "company culture,"…
NotebookLM MCP server management - query notebooks, add from share links, handle auth, reset sessions.
Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected…
Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction.
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels).
Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types.
Implement distributed tracing with Jaeger and Tempo to track requests across microservices and identify performance bottlenecks.
Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices.
Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing…
Clean Architecture and SOLID principles guide. Use this when designing systems, reviewing architecture, or making structural decisions.
When the user wants to improve E-E-A-T, add trust signals, or optimize for expertise and authority. Also use when the user mentions "E-E-A-T," "E-E-A-T signals," "experience…
Create production-ready FastAPI projects with async patterns, dependency injection, and comprehensive error handling.
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3…
Set up Prometheus for comprehensive metric collection, storage, and monitoring of infrastructure and applications.
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.
Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiotropy and choosing among Egger,…
Implement Linkerd service mesh patterns for lightweight, security-focused service mesh deployments. Use when setting up Linkerd, configuring traffic policies, or implemen — from…