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Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five

Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical specs, decision docs, or similar structured content. This workflow helps users efficiently transfer context, refine content through iteration, and verify the doc works for readers. Trigger when user mentions writing docs, creating proposals, drafting specs, or

Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.

Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.

Ferramenta eficiente de busca em banco de dados para o servidor de preprints bioRxiv. Use esta skill para pesquisar preprints de ciências da vida por palavras-chave, autores, intervalos de datas ou categorias, recuperar metadados de artigos, baixar PDFs ou conduzir revisões de literatura.

Use when a user asks for a plan for a coding task, to generate a clear, actionable, and atomic checklist.

Maintain project state across MULTIPLE conversations over days/weeks. Track tasks, decisions, blockers, resources. Auto-update when project mentioned. Generate status reports and proactive reminders.

Automated code review with best practices, security checks, and quality standards.

Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.

Cria diagramas de arquitetura profissionais com tema escuro, como arquivos HTML autônomos com gráficos SVG. Use para solicitações de diagramas de arquitetura de sistema, infraestrutura, nuvem, segurança, topologia de rede ou qualquer diagrama técnico de componentes e suas relações.

Comprehensive GitOps methodology and principles skill for cloud-native operations. Use when (1) Designing GitOps architecture for Kubernetes deployments, (2) Implementing declarative infrastructure with Git as single source of truth, (3) Setting up continuous deployment pipelines with ArgoCD/Flux/Kargo, (4) Establishing branching strategies and repository structures, (5) Troubleshooting drift, syn