Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR.
Master Godot 4 GDScript patterns including signals, scenes, state machines, and optimization. Use when building Godot games, implementing game systems, or learning GDScri — from…
Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational…
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), Google Nano…
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualizati — from…
When the user wants to plan integrated marketing, coordinate channels, or clarify program vs channel vs campaign.
MongoDB with Mongoose — schemas, models, aggregation pipelines, migrations, and Atlas connections. Use when designing collections, writing queries, or integrating MongoDB into…
Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate,…
AI-assisted pair programming with multiple modes (driver/navigator/switch), real-time verification, quality monitoring, and comprehensive testing.
Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by spec — from…
Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices.
Use when implementation is complete, all tests pass, and you need to decide how to integrate the work - guides completion of development work by presenting structured opt — from…
Automated code review analyzing security, performance, maintainability, and test coverage. Activated during code reviews or when conducting analysis.
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and — from…
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit — from…
Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification, and statistical analysis of…
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis def — 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…
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines — from…
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.
Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens.
Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monotonicity criteria.
Design LLM applications using the LangChain framework with agents, memory, and tool integration patterns.
Browser automation CLI for AI agents. Use for website interaction, form automation, screenshots, scraping, and web app verification.
Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing…
Comprehensive testing skill for GabeDA application - designs test strategies (UAT, integration, smoke, unit), creates tests for frontend (React/Playwright) and backend (D — from…
macOS development environment setup wizard. Interactive Q&A to collect preferences, auto-detect installed software, generate customized installation plan.
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology — from…
Remove AI-generated code slop from a branch. Use when cleaning up AI-generated code, removing unnecessary comments, defensive checks, or type casts.
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionarie — from…
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways.
Master ES6+ features including async/await, destructuring, spread operators, arrow functions, promises, modules, iterators, generators, and functional programming patterns for…
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell ty — from…
Comprehensive knowledge system for addiction recovery environments, supporting both residential and outpatient (IOP/PHP) patients.
Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using…
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython.
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/legends/guides collection, panel…
Test web applications with screen readers including VoiceOver, NVDA, and JAWS. Use when validating screen reader compatibility, debugging accessibility issues, or ensuring…
Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering,…
Validate documentation before merging - check completeness, broken links, code example accuracy, and factual correctness.
When the user wants to create, optimize, or audit signup and login pages. Also use when the user mentions "signup page," "login page," "registration page," "auth page," "sign up…
Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a — from…
Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations.
When the user wants to analyze backlinks, audit link profile, or identify link issues. Also use when the user mentions "backlink analysis," "backlink audit," "referring domains,"…
Multi-agent orchestration patterns. Use when multiple independent tasks can run with different domain expertise or when comprehensive analysis requires multiple perspecti — from…
Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing.
When the user wants to create, optimize, or structure a documentation site. Also use when the user mentions "docs," "documentation site," "docs subdomain," "docs.yourdomain.com,"…
Generate images with Google Gemini 3.1 Flash Image Preview (Nano Banana 2) via inference.sh CLI. Capabilities: text-to-image, image editing, multi-image input (up to 14 i — from…
Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation — from…
Comprehensive toolkit for developing with the CocoIndex library. Use when users need to create data transformation pipelines (flows), write custom functions, or operate f — from…
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally i — from…
Analyze Stitch projects and synthesize a semantic design system into DESIGN.md files — from bg-szy/TOP-SKILLS
Specialized knowledge of Bash and Zsh scripting, shell automation, command-line tools, and scripting best practices.
Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB),…
Tailwind CSS v4 principles. CSS-first configuration, container queries, modern patterns, design token architecture. — from bg-szy/TOP-SKILLS
Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens.
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants.
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology.