'stack' 검색 결과

Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.

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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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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 burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Provides expert knowledge for implementing and reviewing application security following OWASP Top 10 (2021), with stack-specific patterns for Spring Boot, Django, Next.js, and Astro.

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Full-stack Convex development guidelines covering React, Vite, TypeScript, mutations, auth, design system, and documentation practices. Use when building features, writing Convex functions, or making code changes in this project.

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Build reactive, type-safe, production-grade backends. ALWAYS use this skill when the user asks to build, plan, design, or implement backend features, APIs, data models, server logic, database schemas, web apps, full stack apps, or mobile apps. This includes planning and architecture discussions.

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Guide for building and refactoring a FastAPI + Prefect + PostgreSQL/pgvector analytics pipeline that extracts insights from chat data using LLM classification, embeddings, UMAP/HDBSCAN clustering, and narrative generation. Use this skill whenever working on this project's codebase — including adding features, refactoring, debugging, creating new endpoints, modifying pipeline stages, or reviewing architecture decisions. Also trigger when the user asks about project structure, stack decisions, async migration, or best practices for this specific system.

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Optimize end-to-end application performance with profiling, observability, and backend/frontend tuning. Use when coordinating performance optimization across the stack.

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Auri: assistente de voz inteligente (Alexa + Claude claude-opus-4-20250805). Visao do produto, persona Vitoria Neural, stack AWS, modelo Free/Pro/Business/Enterprise, roadmap 4 fases, GTM, north star WAC e analise competitiva.

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Cascade merge changes through a chain of dependent branches. Use when updating stacked/chained PRs, propagating changes from a parent branch to all downstream branches, or when the user mentions "cascade merge", "propagate changes", "update dependent branches", or "merge to downstream branches".

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SwiftUI UI component catalog. Use when implementing NavigationStack, Swift Charts, PhotosPicker, TipKit, ScrollView enhancements, animations, layouts, WebView, Liquid Glass and other UI components. Organized by feature category with OS version compatibility info. Reference for discovering available components and implementation patterns.

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Manage Docker containers, images, volumes, networks, and Compose stacks — lifecycle ops, debugging, cleanup, and Dockerfile optimization.

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Tauri 2.x + SolidJS stack for Openrind Desktop native app

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Skill for scaffolding, installation, and composition of shadcn-vue components (based on Reka UI v2). Use when you need to install components, understand Vue variants, compose patterns with vee-validate/Zod, or adapt existing components. Stack: Vue 3 + Reka UI v2 + Tailwind CSS.

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Produz vídeo curto — roteiro, storyboard, prompts por cena e geração via Runway quando há chave. Use quando o usuário disser "vídeo", "reels", "roteiro de vídeo", "Runway", "Higgsfield", "animação", "storyboard", "vídeo de IA". Runway gera de fato a partir de imagem; Higgsfield não tem API pública estável e segue manual. Vídeo é o item mais caro da stack.

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Use when the user wants the project instructions file generated or updated from the detected stack and conventions — 'gerar o arquivo de instruções do projeto', 'criar convenções do projeto', 'setup governance', 'gerar AGENTS'. Writes the shared instructions file read by Claude Code, Codex, Hermes and OpenCode. Do NOT use to analyze the codebase in depth (feat-map) or to initialize the workspace (feat-init).

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Trace bugs backward through call stacks and execution flows to identify the original source of errors, invalid data, or incorrect behavior. Use when debugging complex issues, tracing error origins, investigating data corruption, following execution paths, identifying where invalid data enters the system, or finding root causes of cascading failures.

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Clear the freeze boundary set by /freeze, allowing edits to all directories again. Use when you want to widen edit scope without ending the session. Use when asked to "unfreeze", "unlock edits", "remove freeze", or "allow all edits". (gstack)

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Use when asked to brainstorm, evaluate whether an idea is worth building, run office hours, or think through a new product idea or design direction before any code is written.

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Use when asked to review a plan, challenge a proposal, run a CEO review, poke holes in an approach, think bigger about scope, or decide whether to expand or reduce the plan.

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Weekly engineering retrospective. Analyzes commit history, work patterns, and code quality metrics with persistent history and trend tracking. Team-aware with per-person contributions, praise, and growth areas. Use when asked for weekly retro, what shipped this week, or engineering retrospective.

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