Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-saf — from…
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expec — from…
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions.
Expert at performing task X automatically. Auto-invokes when the user wants to do Y, needs help with Z, or encounters situation W. — from bg-szy/TOP-SKILLS
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (uni — from…
When the user wants indie hacker or bootstrapping founder strategy—growth, channels, Build in Public, or solo founder tactics.
Structured guide for setting up A/B tests with mandatory gates for hypothesis, metrics, and execution readiness. — from bg-szy/TOP-SKILLS
Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST…
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R).
Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns.
Conduct thorough, constructive code reviews for quality and security. Use when reviewing pull requests, checking code quality, identifying bugs, or auditing security.
Implement web accessibility (a11y) standards following WCAG 2.1 guidelines. Use when building accessible UIs, fixing accessibility issues, or ensuring compliance with dis — from…
Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing…
Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies — from bg-szy/TOP-SKILLS
Create AI avatar and talking head videos with OmniHuman, Fabric, PixVerse via inference.sh CLI. Models: OmniHuman 1.5, OmniHuman 1.0, Fabric 1.0, PixVerse Lipsync.
Automate Google NotebookLM - create notebooks, add sources, generate podcasts/videos/quizzes, download artifacts.
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions.
Create a topic-specific GitHub awesome-list repository scaffold with a polished README, concise contribution rules, AI-agent instructions, URL verification, license, and reusable…
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and qual — from…
Generate AI videos with Google Veo, Seedance, Wan, Grok and 40+ models via inference.sh CLI. Models: Veo 3.1, Veo 3, Seedance 1.5 Pro, Wan 2.5, Grok Imagine Video, OmniHu — from…
Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence).
Use when you have a written implementation plan to execute in a separate session with review checkpoints — from bg-szy/TOP-SKILLS
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating — from…
Coordinator workflow for orchestrating dockeragents through fix-review-iterate-present loop. Use when delegating any task that produces code changes.
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…
Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer.
Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH…
Perform comprehensive code reviews covering security, style, performance, and best practices. Use when reviewing code changes before commit or merge, auditing existing code, or…
Batteries-included agent component for React/Next.js from ui.inference.sh. One component with runtime, tools, streaming, approvals, and widgets built in.
Discovers periodic signals of unknown period in time-series omics data using Lomb-Scargle periodograms (scipy), autocorrelation, and wavelet time-frequency decomposition (pywt).
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical sig — from…
Configure secure, high-performance connectivity between on-premises infrastructure and cloud platforms using VPN and dedicated connections.
Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA/plasmid, AAV6), sizing homology arms, placing the cut…
Guide for creating new skills in Kai's personal AI infrastructure. Use when user wants to create, update, or structure a new skill that extends capabilities with specialized…
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications.
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and ident — from…
When the user wants to run CTV, OTT, or streaming TV ads. Also use when the user mentions "CTV ads," "connected TV," "OTT advertising," "streaming ads," "TV ads," "Hulu ads,"…
Master modern React state management with Redux Toolkit, Zustand, Jotai, and React Query. Use when setting up global state, managing server state, or choosing between sta — from…
Use when user asks 'how should I...' or 'what's the best approach...' after exploring code, OR when you've tried to solve something and are stuck, OR for unfamiliar workflows, OR…
Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR.
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Master SQL query optimization, indexing strategies, and EXPLAIN analysis to dramatically improve database performance and eliminate slow queries.
Master monorepo management with Turborepo, Nx, and pnpm workspaces to build efficient, scalable multi-package repositories with optimized builds and dependency management.
Comprehensive testing strategies for Guts including unit tests, integration tests, property-based testing, and fuzzing — from bg-szy/TOP-SKILLS
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresent — from…
Write and maintain Architecture Decision Records (ADRs) following best practices for technical decision documentation.
Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment.
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network.
Render videos from React/Remotion component code via inference.sh. Pass TSX code, get MP4. Supports all Remotion APIs: useCurrentFrame, useVideoConfig, spring, interpolat — from…
End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding.
Configure Turborepo for efficient monorepo builds with local and remote caching. Use when setting up Turborepo, optimizing build pipelines, or implementing distributed ca — from…
Generate images with Google Nano Banana 2 (Gemini-family flash-tier text-to-image) on RunComfy — bundled with the model's documented prompting patterns so the skill gets sharper…
Master Python asyncio, concurrent programming, and async/await patterns for high-performance applications.
Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor…
Update all documentation in .plans, CLAUDE.md files, docs, and .tasks to match current codebase state.
When the user wants to configure canonical URLs, fix duplicate content, or consolidate URL signals. Also use when the user mentions "canonical," "canonical URL," "duplicate…
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions.
Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value…
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction.
Senior FDA consultant and specialist for medical device companies including HIPAA compliance and requirement management.