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sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.

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Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().

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Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

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This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.

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Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

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The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

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This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

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Issue 池全生命周期管理（开发范式 v1 规划段）。核心是一条 issue 驱动的流程：用户随手丢想法，你把糊的 issue 变成能开工的 task——产出的是“问题定义”，不是“解决方案实现”；载体就是仓库根的 ISSUES.md。五个动作：记、并、拆、转、pending。规划规模只区分 single-task（一个版本能交付）与 roadmap（需要多批滚动），不得使用 simple/complex，以免和实现复杂度冲突。

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Checks whether a company's own website mentions a specific keyword, using one simple Google site: query per keyword through a SERP API, and turns the hit into a copy-ready line. Triggers on "does their site mention X", "site: search", "find companies whose website says X", "filter this list by a keyword on their site", "check if they talk about X", "google search enrichment". Outputs site_keyword_hit plus a one-clause personalization line with an evidence URL.

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Applies the SUCCESs Framework from Made to Stick by Chip Heath and Dan Heath. Use when crafting messages that need to be remembered, writing pitches, creating presentations, designing training materials, telling stories that drive action, or diagnosing why a message isn't landing. The six principles (Simple, Unexpected, Concrete, Credible, Emotional, Stories) diagnose and fix communication failures. Triggers include 'how do I make this memorable', 'my pitch isn't landing', 'people forget what we told them', 'how do I tell a better story', 'our training materials are boring', 'how do I present data compellingly', 'nobody remembers our message', 'how do I get people to care about this', 'my writing is too abstract'. NOT for channel selection (use Traction), not for brand messaging structure (use StoryBrand), not for positioning (use Obviously Awesome).

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Use when the user mentions Higgsfield Canvas, a node-based or node graph workspace, an infinite board/canvas, chaining generations into a pipeline, or wants to wire prompts → images → videos across models on one surface. Covers what Canvas is, the node categories, the seven models that run inside Canvas, the named canvas patterns (Simple Seedance, Extend Video, Image Edit, StoryBoard With Elements, Long Video fan-out), the build-free / generate-paid cost model, reusable templates, assets-as-nodes, and Shared Canvas live collaboration. Also trigger on 'Higgsfield ComfyUI alternative', 'node workflow', or 'connect nodes to build a scene/campaign'.

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Use this skill when the user wants an evidence-based research memo, literature review, market/policy/technical landscape, or a multi-source decision brief with citations, trade-offs, and a clear conclusion. Best for tasks that need synthesis across multiple external sources, iterative follow-up research, or a reusable written artifact. Do not use for quick factual lookups, single-source summaries, simple Q&A, summarizing one document the user already provided, plan-only requests where the user explicitly defers the actual research, or when the user wants a short answer with no need for cited evidence (a short but evidence-backed conclusion is still a brief memo, which this skill covers). Chinese trigger examples: "帮我调研", "深度研究", "综述报告", "技术选型分析", "竞品研究", "政策分析".

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Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines.

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Scaffolds a structured investigation in scratch/ for empirical research and documentation. Use when the user says "start an investigation" or wants to: trace code paths or data flow ("trace from X to Y", "what touches X", "follow the wiring"), document system architecture comprehensively ("document how the system works", "archeology"), investigate bugs ("figure out why X happens"), explore technical feasibility ("can we do X?"), or explore design options ("explore the API", "gather context", "design alternatives"). Creates dated folder with README. NOT for simple code questions or single-file searches.

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Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.

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Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.

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Coordinate nontrivial work in the ctx repository when a task has independent investigation, implementation, or test lanes; compute-heavy checks; or repetitive changes suited to scripts or codemods. Use for decomposition and concurrency decisions, not simple edits or questions.

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Builds tables and data grids for displaying tabular information, from simple HTML tables to complex enterprise data grids. Use when creating tables, implementing sorting/filtering/pagination, handling large datasets (10-1M+ rows), building spreadsheet-like interfaces, or designing data-heavy components. Provides performance optimization strategies, accessibility patterns (WCAG/ARIA), responsive designs, and library recommendations (TanStack Table, AG Grid).

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Lazy senior dev mode: the smallest change that fully solves the task, and a reply a busy human understands in one read. Use on any coding task (writing, fixing, refactoring, reviewing, choosing dependencies) and when the user says "ponytail", "be lazy", "simplest solution", "yagni", or complains about over-engineering or bloat. Levels: lite, full (default), ultra.

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Kimi Browser Extension（Kimi 浏览器扩展，原 Kimi WebBridge）lets AI control the user's real browser — navigate, click, type, read, screenshot, and interact with any website using the user's actual login sessions. Use this skill whenever the user wants to interact with websites, automate browser tasks, scrape web content, or perform any action requiring a real browser. Also use when the user mentions "browser", "webpage", "open URL", "screenshot", asks to read/interact with any website, or wants a reusable CLI tool or script that automates a specific website. Use even for simple-sounding browser requests — the daemon handles all complexity.

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Guide for modernizing and migrating MSBuild project files to SDK-style format. USE FOR: converting legacy .csproj/.vbproj with verbose XML to SDK-style, migrating packages.config to PackageReference, removing Properties/AssemblyInfo.cs in favor of auto-generation, eliminating explicit Compile Include lists via implicit globbing, consolidating shared settings into Directory.Build.props. Indicators of legacy projects: ToolsVersion attribute, an Import of Microsoft.CSharp.targets via $(MSBuildToolsPath), .csproj files over 50 lines for simple projects. DO NOT USE FOR: projects already in SDK-style format, non-.NET build systems (npm, Maven, CMake), .NET Framework projects that cannot move to SDK-style.

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Use Metalint in .NET repositories that ship Node-based frontend assets and want one CLI entrypoint over several underlying linters. USE FOR: unified frontend lint commands; combined ESLint, Stylelint, HTMLHint, or similar checks; CI orchestration over multiple frontend linters. DO NOT USE FOR: simple repos where Biome already covers the required surface; teams that have not decided which underlying linters own each file type. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Use the open-source free `Stryker.NET` mutation testing tool for .NET. Use when a repo needs to measure whether tests actually catch faults, especially in critical libraries or domains. USE FOR: the repo uses or wants Stryker.NET; mutation testing is needed for high-risk code. DO NOT USE FOR: every PR path by default in a large repo; simple coverage collection. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Plan complex Blazor UI features by decomposing them into focused components. USE FOR: building a complex Blazor page with multiple sections, planning component decomposition, designing a multi-section dashboard or layout, breaking down a large UI feature into composable components, pages with sidebars and content panels, any page with 3+ distinct visual sections or multiple interacting sub-features, identifying parent-child relationships and data flow. DO NOT USE FOR: creating new Blazor projects or apps from scratch (use create-blazor-project), implementing a single individual component (use author-component), writing component code with parameters and EventCallback (use author-component), or simple single-component pages.

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