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We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positi

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mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of g

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This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BS

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Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

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Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including

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The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualizati

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seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

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基于 TrailSnap（行影集）现有设计系统设计、实现和审查前端 UI。适用于 package/website 的新页面、组件、布局、主题、移动端适配与界面改版；纯后端任务和其他项目不适用。

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Design and build expressive 3D scenes, explainers and interactive models with grounded subject knowledge. Use for 3D creation or edits, including scientific visualization and spatial puzzles.

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Web 视觉设计 SKILL。输入 PRD / 参考 URL / 截图 / 关键词（任意组合），先产出一份标准化 DESIGN.md 设计规范，用户确认后据此生成 UI/UX、视觉、动效、响应式全部达标的 web 代码。专攻 web 端：Landing Page、Portfolio、产品页、博客、个人站、SaaS 介绍页等。当用户说"帮我做个网站""设计一个页面""参考 XX 做一个""把这个截图/PRD 做成网页""做一个 landing page""出一份 design 规范"时触发。不用于后端、数据库、纯逻辑 bug 修复。

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网页设计与部署。生成精美的单页 HTML 网页（报告、落地页、数据可视化等），支持一键部署到 Cloudflare Pages。使用 Tailwind CSS + Chart.js + Font Awesome 技术栈。当用户要求制作网页、生成报告页面、创建落地页、数据可视化展示、部署网页到线上时使用。

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设计、诊断和迭代产品或品牌 Logo，从定位与审美反馈收敛方向，完成应用图标适配、品牌组合和可直接使用的资产。适用于“做个 logo”“这些版本不好看”“沿这个方向精修”“导出可用图标”；不用于普通页面 UI、整站设计或单纯插画。需在 Codex 中使用（依赖其图像生成）。

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和用户一起敲定一个前端页面的整页方案（三层法：先定这页给用户什么，再定含哪几样怎么排，最后才是长什么样），最后打成一个定稿包（含高保真全状态与交互流程图）交给开发。触发：用户对一个页面说「想重做 / 重新设计 / 整页不对 / 太满 / 说不清具体改哪」，或「我们讨论一下这页怎么设计」。覆盖三种情形：① 已有页面整页重做；②「替换」——新方案占用同一个入口（同一路由 / 同一侧栏条目）且用户拿着现行页面在说话，功能变不变不作判据；把几个同性质页面合成一页、占其中一个入口，也算替换；③ 从零的新页面，走同一套流程，第 0 步的问法按「新页面」那一栏改。不适用于：只改一两处具体元素的具体属性（间距大一点、按钮换色、换个图标）——这种直接改，不必起流程；照着截图或设计图 1:1 复刻；写 PRD / 测试用例（本 skill 的定稿包是它们的输入）；没有界面的架构 / 数据 / 流程方案；跨页的信息架构 / 导航分组 / 侧栏结构——本 skill 的作用域限单个页面之内。已有页面补状态（加载 / 空 / 错误 / 未设置）：只补一两个且常态布局不动 → 直接改；要成套补齐、或补状态时发现常态布局本身要改 → 用本 skill。

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和用户一起把一个功能「看不见的部分」敲定：数据存哪、谁写谁读、怎么加载、怎么保存、默认值和升级、核心执行规则、出问题时怎么办、旧东西怎么迁。每条规则带编号、案例和状态（已定 / 方案里有但你没拍板 / 待你定 / AI 定），用户只回答带案例的新选择题、过目没拍过板的规则；给用户看的是按「你会问的问题」分组的问答卡片（最绕的逻辑配可点的模拟器）；最后请另一家模型只读查边界，问题闭环后封成后端逻辑包，PRD、测试用例和代码审核按规则编号追溯。触发：前端交互已定、用户说「还有很多后端逻辑 / 加载 / 配置要讲清楚」「有没有遗漏的边界条件」「规则讲清楚」；或没有界面但规则复杂的功能（调度、同步、配置、额度、迁移）。分三档用：规则多且互相影响出完整包；少量清楚的变化只出规则表；行为不变的技术修复跳过。不适用于：页面长什么样、怎么排（用 page-solution-design）；写 PRD / 测试用例（本 skill 的规则包是它们的输入）；纯代码重构、性能调优、架构巡检报告。

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Point at something on the human's macOS screen with a big arrow and a sign ("Franz, click HERE") using the bigarrow CLI. Use whenever the human has to look at, click, type into or choose a specific spot, button, field, window, tab or menu: show me where, point to it, which button, where do I click, zeig mir wo, guide me through this UI, the human must approve or sign something, or you need the human's hand and they may not be looking at the terminal. Mandatory when it is time-critical: a code that expires, a login or payment page that times out, a build waiting on the human.

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Amazon Store builder — page layouts, brand story, shoppable images, traffic driving, conversion optimization

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Framework for running single-variable cold email experiments. Defines experiment types (list-only, copy-only, combined), confidence weighting, minimum sample sizes, and success criteria. Use when the user wants to improve a campaign, test a new list vs old one, or compare copy variants. Prevents the

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Upload a CSV of leads + a variants YAML (produced by /campaign-copywriting) to Smartlead as a DRAFT campaign. Handles tag-scoped inbox selection, A/B/C variant assembly, custom field mapping, schedule config, and batch lead upload. ALWAYS creates in DRAFT — you review in Smartlead UI and hit Start manually. Use after /campaign-copywriting, just before the campaign goes live.

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Use when a user gives or references a webpage URL and wants to extract, reproduce, port, or locally replay a WebGL, WebGPU, Canvas, shader-like, animated background, interactive 3D, or web visual effect. Locks the target rendering surface group, records shader/resource/render graph/timing/input evidence, builds an evidence-matched local baseline, then projectizes it. Do not use for ordinary DOM/CSS page cloning.

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Design the optimal funnel from click to conversion. Trigger on "funnel", "conversion path", "booked calls".

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Create a packaging design brief — structure, visual direction, hierarchy, materials, and unboxing experience. Use when the user says "packaging design", "packaging brief", "product packaging", "packaging direction", "label design", "packaging identity", "unboxing experience", "packaging look and feel", "brief my packaging designer", "packaging for my product", "packaging strategy", "retail packaging", "e-commerce packaging", "what should my packaging look like", or is briefing a designer, agency, or manufacturer on packaging requirements.

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Create a visual identity brief for a brand — logo direction, color palette, typography, imagery style, and design system foundations. Use when the user says "visual identity", "brand identity", "logo brief", "logo direction", "design brief", "brand design", "color palette for my brand", "typography for my brand", "visual language", "design system", "brand look and feel", "what should my brand look like", or is briefing a designer or design agency. Also use when the user has a brand strategy and wants to translate it into visual design direction.

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Create a comprehensive brand standards document — covering logo usage, color, typography, voice, messaging, and application rules. Use when the user says "brand guidelines", "brand standards", "brand book", "style guide", "brand guide", "brand manual", "brand rules", "brand documentation", "brand toolkit", "onboarding designers or copywriters", "need a document for the team", "brand consistency across teams", or wants to codify all brand decisions into a reusable reference document.

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Make frontend output look intentional, not AI-generated. Use for any UI work — components, pages, layouts.

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