Automated coordination, formatting, and learning from Claude Code operations using intelligent hooks with MCP integration.
Use when authoring or repairing a coordinate-explicit JSON specification for an editable PPTX deck.
Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction.
Technical leadership guidance for engineering teams, architecture decisions, and technology strategy.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…
Generate and edit images with OpenAI GPT Image 2 (ChatGPT Images 2.0) on RunComfy. Documents GPT Image 2's strengths (embedded text, logos, multilingual typography, instr — from…
Create AI avatar and talking head videos via inference.sh CLI. Recommended: P-Video-Avatar (fastest, cheapest, built-in TTS). Also: OmniHuman, Fabric, PixVerse.
Generate user-friendly release notes from git commits. Use this when preparing releases, writing changelogs, or summarizing development progress.
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications.
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images.
Assigns isolate identity at the right resolution for the question -- ANI / Mash species triage, 7-locus MLST historical comparability, cgMLST / wgMLST outbreak resolution…
Use when Codex, Hermes, OpenClaw, Claude Code, Cowork, or another AI agent needs to plan, review, implement, audit, or improve email work focused on campaign briefs, audi — from…
Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), severity classification,…
Schedule alarms and countdown timers in iOS apps using AlarmKit. Use when implementing alarm functionality, timer features, AlarmKit integration, snooze/stop controls, Dynamic…
You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior.
Extract text and tables from PDF files, fill forms, merge documents. Use when working with PDF files or when the user mentions PDFs, forms, or document extraction.
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files.
API documentation workflow for generating OpenAPI specs, creating developer guides, and maintaining comprehensive API documentation. — from bg-szy/TOP-SKILLS
Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific…
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identif — from…
Master advanced Git workflows including rebasing, cherry-picking, bisect, worktrees, and reflog to maintain clean history and recover from any situation.
Complete Git workflow from conventional commits to pre-completion verification. Use for all Git operations including commits, branches, and releases.
Extract and analyze data from invoices, receipts, bank statements, and financial documents. Categorize expenses, track recurring charges, and generate expense reports.
Master SQL query optimization, indexing strategies, and EXPLAIN analysis to dramatically improve database performance and eliminate slow queries.
Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST),…
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…
Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies.
Expert guide on prompt engineering patterns, best practices, and optimization techniques. Use when user wants to improve prompts, learn prompting strategies, or debug age — from…
Debug regex patterns with visual breakdowns, plain English explanations, test case generation, and flavor conversion.
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section — from…
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
Use when starting any conversation - establishes mandatory workflows for finding and using skills, including using Read tool before announcing usage, following brainstorm — from…
Serena MCP for project memory and code navigation. Use when managing Serena memories, navigating symbols, performing intelligent refactoring, or maintaining context/continuity…
Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and…
Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and…
Extracts and analyzes competitors' ads from ad libraries (Facebook, LinkedIn, etc.) to understand what messaging, problems, and creative approaches are working.
Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP (Puillandre 2021 successor to ABGD), mPTP C++ (Kapli 2017…
Update all documentation in .plans, CLAUDE.md files, docs, and .tasks to match current codebase state.
Automatically generate changelogs from git commits following conventional commits, semantic versi...
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit — from…
Generate images with Alibaba Qwen-Image-2.0-Pro via inference.sh CLI. Professional text rendering, fine-grained realism, enhanced semantic adherence.
When the user wants to design, optimize, or audit website footers. Also use when the user mentions "footer," "page footer," "site footer," "footer links," "footer navigation,"…
Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction.
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arb — from…
Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate…
Create structured incident response runbooks with step-by-step procedures, escalation paths, and recovery actions.
A skill for analyzing data using Python (pandas) and generating professional visualizations (matplotlib/seaborn).
Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation.
Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin.
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR stu — from…
Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR…
Software architecture and UI/UX principles for building genuinely new solutions, not derivative work.
Generate AI chat completions using GPT-4o through the verging.ai proxy API with streaming (SSE) and non-streaming response support.
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…
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels.
Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra.
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expec — from…
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse. — from bg-szy/TOP-SKILLS