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Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

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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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Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained f

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This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and qua

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Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualiz

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Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a

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Point Aeon at a service's /feedback endpoint - pull what agents reported (bugs, missing features), triage and cluster it, then build the best accepted request as a PR for a human to approve.

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Plan and execute substantial multi-file builds, features, migrations, and refactors with Astra as orchestrator and DeepSeek V4.1 Flash as the native Codex implementation worker. Use for phased planning and delegated build execution, including existing Superpowers or GSD plans. Skip trivial edits and explicitly single-agent tasks. Worker children must not invoke this orchestration skill.

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Run the fixed 6-step session-opening sequence — pwd, read progress, git log, count remaining features, init.sh, smoke-test last feature — before touching any new work. The orientation ritual that lets fresh-context sessions reconstruct project state in under a minute.

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Read git log since initial scaffold + last 3 progress notes, draft feature additions to a SEPARATE suggestions file so feature_list.json stays immutable

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Applies Eric Ries's Lean Startup methodology for building products under extreme uncertainty. Use when iterating toward product/market fit, designing MVPs, deciding whether to pivot or persevere, setting up actionable metrics, or accelerating the Build-Measure-Learn loop. Triggers include 'how do we test this idea fast', 'what should our MVP look like', 'our metrics look good but we're not growing', 'should we pivot', 'we're building features no one uses', 'how do we measure validated learning', 'vanity metrics vs real metrics', 'how to do innovation accounting'. NOT for companies with proven product/market fit scaling a known playbook (use Crossing the Chasm), not for determining Market Type (use Four Steps), not for sales methodology (use SPIN Selling), not for pricing strategy (use Monetizing Innovation).

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Create comprehensive HTML architecture diagrams showing data flows, business objectives, features, technical architecture, and deployment. Use when users request system architecture, project documentation, high-level overviews, or technical specifications.

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Use when writing, reviewing, refactoring, or planning Flutter/Dart code — screens, features, project structure, state management, folders, widgets, cubits/blocs, repositories, services, or tests.

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Use when positioning needs defining or sharpening — a statement built on Promise, Proof, and Path, a differentiation matrix against competitors, category entry points, a three-level message hierarchy, and tagline directions. Trigger on 'positioning', 'positioning statement', 'what makes us different', 'USP', 'why should customers choose us over them', 'we sound the same as everyone else'. Also use when the user can list features but not a reason to pick them. Not for — competitor teardown research, see `08-competitor-research-global`; how the brand sounds in writing, see `35-brand-voice-global`; the offer and its value stack, see `31-offer-design-global`; the launch built on it, see `59-go-to-market-global`.

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You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.

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Use when completing tasks, implementing major features, or before merging to verify work meets requirements

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Generates user-facing changelogs and release notes from git commit history. Parses conventional commits, categorizes changes into features, fixes, breaking changes, and more, then rewrites technical messages into customer-friendly language. Use when the user asks to generate a changelog, write release notes, summarize recent commits, prepare CHANGELOG.md, or document what changed between versions.

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Use after a phase executes, when the user wants to test the built features themselves. Runs one conversational UAT test at a time into {phase}-UAT.md and, when something fails, diagnoses it and queues fix plans for /gsd-execute-phase.

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Implement, review, or improve SwiftUI features using the iOS 26+ Liquid Glass API. Use when asked to adopt Liquid Glass in new SwiftUI UI, refactor an existing feature to Liquid Glass, or review Liquid Glass usage for correctness, performance, and design alignment.

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Use when completing tasks, implementing major features, or before merging to verify work meets requirements

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Use when building AI features into a product: LLM integration, RAG pipelines, guardrails, streaming, AI UX, prompt engineering, or AI cost control. Treats prompts as code and validates every model output.

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You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.

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Test-driven development with red-green-refactor loop. Use when user wants to build features or fix bugs using TDD, mentions "red-green-refactor", wants integration tests, or asks for test-first development.

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Structure Next.js projects with Feature-Sliced Design layers, domain-grouped slices, and strict import hierarchy. Use when organizing features into FSD layers, enforcing slice boundaries, or keeping page.tsx thin.

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