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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE for visualization. Covers the type-vs-state marker distinction (cluster on lineage, test state within clusters), over-provision-then-metacluster, the Weber-Robinson benchmark, seed dependence and metacluster stability, why embeddings are for looking not measuring, and median-heatmap annotation/merging. Use when discovering populations without predefined gates, choosing a clustering algorithm, selecting the number of metaclusters, or annotating clusters into cell types.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Plan and report authorized vulnerability assessments on owned systems. Prioritize evidence, severity, and remediations. Do not deliver exploit payloads.

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Use when adding hypermedia links to REST responses, building self-describing APIs, or implementing Spring HATEOAS. Use when you see EntityModel, CollectionModel, or RepresentationModel in the project.

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Provides expert knowledge for building modern native Android apps using Kotlin, Jetpack Compose, Material Design 3, MVI architecture, Hilt dependency injection, and Media3/ExoPlayer.

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Writing style guide for technical content, social media, blog posts, READMEs, git commits, and developer documentation. Optimized to avoid AI detection patterns. Use when writing any content beyond code.

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You are an accessibility expert specializing in WCAG compliance, inclusive design, and assistive technology compatibility. Conduct audits, identify barriers, and provide remediation guidance.

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Extract typical annual GPP, annual evapotranspiration, mid-season LAI, mid-season root biomass, mid-season shoot biomass, median canopy height, maximum primary-root depth, Vcmax at 25oC, and Jmax at 25oC from EcoSIM h0 NetCDF output files. Use when asked to derive these EcoSIM output targets from a selected .ecosim.h0.*.nc file for model-output processing, trait checks, or benchmark summaries.

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Investigate implementation failures using root-cause-first debugging. Use when an implementer is blocked, verification fails, or repeated remediation does not converge.

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Review a task implementation against approved specs, task boundaries, and verification evidence. Use after an implementer finishes a task, after remediation, or before accepting a task as complete.

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Accessibility auditing and remediation skill for Vue 3 + Reka UI. Use when reviewing components, verifying WCAG 2.1 AA, fixing ARIA issues, or validating keyboard navigation in Reka UI components.

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Escreve copy para redes sociais — post avulso, carrossel, thread e legenda — respeitando limite, formato e cultura de cada plataforma. Use quando o usuário disser "post para", "legenda", "conteúdo para LinkedIn", "carrossel", "social media", "adaptar para as redes", "texto do Instagram". Para o gancho isolado ver copy-hooks; para derivar de material existente ver copy-repurpose.

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Organize, categorize, rename, and manage files systematically using automated rules, naming conventions, and folder structures for efficient file management. Use when organizing uploaded files, implementing file naming conventions, categorizing files by type or metadata, creating folder structures, cleaning up messy directories, automating file movements, implementing media libraries, or building file management systems.

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When the user wants help with paid advertising campaigns on Google Ads, Meta (Facebook/Instagram), LinkedIn, Twitter/X, or other ad platforms. Also use when the user mentions 'PPC,' 'paid media,' 'ROAS,' 'CPA,' 'ad campaign,' 'retargeting,' 'audience targeting,' 'Google Ads,' 'Facebook ads,' 'LinkedIn ads,' 'ad budget,' 'cost per click,' 'ad spend,' or 'should I run ads.' Use this for campaign strategy, audience targeting, bidding, and optimization. For bulk ad creative generation and iteration, see ad-creative. For landing page optimization, see page-cro.

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When the user wants to plan a content strategy, decide what content to create, or figure out what topics to cover. Also use when the user mentions "content strategy," "what should I write about," "content ideas," "blog strategy," "topic clusters," "content planning," "editorial calendar," "content marketing," "content roadmap," "what content should I create," "blog topics," "content pillars," or "I don't know what to write." Use this whenever someone needs help deciding what content to produce, not just writing it. For writing individual pieces, see copywriting. For SEO-specific audits, see seo-audit. For social media content specifically, see social-content.

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Auto-review pipeline — reads the full CEO, design, eng, and DX review skills from disk and runs them sequentially with auto-decisions using 6 decision principles. Surfaces taste decisions (close approaches, borderline scope, codex disagreements) at a final approval gate. One command, fully reviewed plan out. Use when asked to "auto review", "autoplan", "run all reviews", "review this plan automatically", or "make the decisions for me". Proactively suggest when the user has a plan file and wants to run the full review gauntlet without answering 15-30 intermediate questions. (gstack) Voice triggers (speech-to-text aliases): "auto plan", "automatic review".

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Import a single webpage from any URL into canonical EDS block format — structured HTML that authors edit in DA. Scrapes the page, analyzes structure, maps to existing blocks, and generates HTML for immediate local preview. Also triggered by terms like "migrate", "migration", or "migrating". Use this when the goal is canonical EDS authoring; use the snowflake skill instead when the user wants to preserve the original DOM byte-for-byte (static-to-EDS overlay).

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Create any visual design using Adobe Express templates — including flyers, posters, banners, social media posts (Instagram stories, Facebook posts, LinkedIn graphics), business cards, invitations, greeting cards, resumes, cover letters, brochures, newsletters, certificates, presentations, YouTube thumbnails, email headers, logos, menus, labels, and more. Use this skill whenever the user wants to make, design, create, or build any visual — even if they just say "make me a flyer", "design a poster", "I need something for Instagram", "create an event invite", "make a business card", or any similar request. Also handles requests to find or browse templates, edit text/copy, change background colors, or animate a design. Access: 🔐 Signed-In required | Gen AI: ❌

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Resize photos and videos to exact pixel dimensions or aspect ratios using Adobe tools. Use this skill whenever a user wants to resize, scale, or change the dimensions of an image or video file — including phrases like "resize this to 1920x1080", "make this 4K", "scale to 800x600", "change the aspect ratio to 16:9", "resize my video", "make the image smaller", "crop to square", "fit this to a specific size", "resize for print", "resize for web", "make it 300 DPI ready", "change canvas size", "resize a batch of photos", or any request specifying target dimensions (W×H, ratio, or named size like "4K", "HD", "A4"). Also triggers for: "make this fit a specific size", "resize to [any dimension]", "I need this at [WxH]", "scale my video down", "change resolution", "downscale", "upscale". NOT for social media platform sets (use adobe-create-social-variations for that). Uses image_crop_and_resize for photos, video_resize for videos.

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Audit an AEM Edge Delivery Services page for content quality, SEO, accessibility, performance, and EDS best practices. Produces a prioritized fix list with specific remediation steps. Use when reviewing page quality, preparing for launch, or optimizing existing content.

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