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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Capture and review Agent Skill observations, and create, run, diagnose, or iteratively improve Skill evaluations (evals) with the skill-up CLI. Use when the user asks to record explicitly attributed Skill usage or feedback; review observations or user-supplied traces/transcripts; turn an approved observation into a regression case; evaluate, test, regress, verify, fix, improve, iterate, or evolve a Skill; add or strengthen eval cases; write eval.yaml/case.yaml; run skill-up run/validate/list-cases/report/import/init; or migrate from Anthropic evals.json. Plugin observation capture/review require either the Codex skill-up plugin or an observer-enabled DSH skill-up plugin. User-supplied external evidence can be reviewed without a plugin; evaluation remains multi-engine.

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Build CarPlay-enabled apps using the CarPlay framework. Use when creating navigation, audio, communication, EV charging, parking, or food ordering apps for the car display, working with CPTemplateApplicationScene, CPInterfaceController template hierarchies, CPListTemplate, CPMapTemplate, CPNowPlayingTemplate, configuring CarPlay entitlements, or integrating with CarPlay Simulator for testing.

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Deep competitive intelligence for any market. Analyzes competitors' products, pricing, customer sentiment, GTM strategy, and growth signals using real web data. Produces battle cards, pricing landscape, and feature matrix. Use when the user wants to understand their competitive landscape, analyze competitors, compare products in a market, or research who they're competing against. Triggers for "who are my competitors", "competitive analysis", "competitor research", "battle cards", "pricing comparison", "competitor pricing", "market players", "competitive intelligence", "competitive landscape", "who else is in this space", "competitive moat", or any request to profile, compare, or map competitors in a category. Works standalone — no prior startup-design session needed.

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Microstrip, stripline, CPW, differential pairs, and crosstalk analysis for impedance-controlled PCB interconnects. TRIGGER: user asks to design or analyze a transmission line (microstrip, stripline, CPW, coplanar, differential pair), extract RLGC or per-unit-length parameters, compute trace impedance, analyze a PCB trace cross-section, or perform crosstalk/coupling analysis. Invoke BEFORE writing code — preferred over RF Toolbox analytical functions (txlineMicrostrip, txlineStripline, txlineCPW). SKIP: EM simulation/S-parameter extraction of an existing component (use matlab-analyze-em), material/stackup definition only (use matlab-manage-pcb-material), building custom non-catalog geometry (use matlab-assemble-pcb-layout), optimization sweeps (use matlab-optimize-pcb-design).

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Select and use Audio Toolbox acoustic, psychoacoustic, and speech quality metrics. Use when computing loudness, sharpness, roughness, fluctuation strength, noise criteria (NC/RNC/RC), speech transmission index (STI), speech intelligibility index (SII), speech quality (ViSQOL, STOI), SPL, reverberation time (RT60), tone-to-noise ratio, or prominence ratio. Also use when asked about PESQ, POLQA, calibration factor, EBU R 128, LUFS, HVAC noise, background noise evaluation, or how to measure audio quality or noise compliance. Covers calibration, standard selection, signal alignment, and the complete function inventory including what does NOT exist.

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Integrate antennas into RF systems using MATLAB Antenna Toolbox and RF Toolbox. Covers impedance matching network design (L/Pi/Tee topologies, evaluation parameters, Richards transformation), measured antenna creation (E-field, directivity-only, EmbeddedE, ffsReader import), RF propagation and site planning (txsite/rxsite, coverage, SINR, ray tracing, link budget), and SAR estimation (birdcage+Phantom, conformalArray+Custom3D, direct EHfields). Use when the user wants to match an antenna, create a measuredAntenna, compute coverage or signal strength, perform ray tracing, or estimate SAR.

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Perform time-frequency analysis in MATLAB using CWT, STFT, synchrosqueezing, reassignment, wavelet coherence, cross spectrogram, EMD/VMD, multiresolution analysis, and time-frequency filtering. Triggers on: time-frequency, spectrogram, scalogram, cwt, stft, istft, fsst, wsst, wcoherence, xspectrogram, modwt, modwtmra, modwpt, emd, vmd, hht, tffilt, dgt, gabor, instantaneous frequency, synchrosqueezing, reassignment, ridge extraction, wavelet coherence, cross spectrum, mode decomposition, signal decomposition, time-frequency filtering.

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Perform aerospace unit conversions, time conversions, coordinate frame transformations, and rotation representations using Aerospace Toolbox. Use when converting units (length, velocity, angle, acceleration, angular velocity, force, mass, pressure, temperature, density), computing Julian dates or decimal years, transforming between coordinate frames (ECEF, ECI, LLA, flat Earth, geodetic/geocentric, NED, body, wind, stability), or working with rotation representations (Euler angles, DCM, quaternion, Rodrigues vector). Also use when the user asks about aerospace coordinate systems, reference frames, or rotation conventions.

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Build and strengthen your e-commerce brand identity. Brand positioning, messaging, visual identity guidelines, and brand consistency across sales channels and marketing touchpoints.

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Create comprehensive business strategy with premise deconstruction, business model stress test, pricing, go-to-market plan, and competitive positioning. Runs a 4-layer premise audit before strategy, then generates a full market research report with SWOT, 4P, 10-point business model validation, and constraint analysis. Use when the user has an idea and needs a strategic plan, competitive analysis, pricing strategy, GTM plan, or says 'business plan', 'strategy', 'pricing', 'go-to-market', or 'competitive analysis'.

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When the user wants to choose an SEO-friendly domain for a new site—brand vs keyword domain, TLD selection, or domain best practices. Also use when the user mentions "domain choice," "pick domain," "SEO-friendly domain," "brand domain," "EMD," "PMD," "exact match domain," "partial match domain," "TLD," ".ai domain," ".com vs .io," "domain length," "domain history," or "defensive domain registration." For migration, use rebranding-strategy.

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When the user wants to write, audit, or optimize a meta description, SEO description, SERP snippet candidate, duplicate description, description length, or description rewrite issue. For a sitewide metadata lifecycle including implementation and production validation, use page-metadata.

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When the user wants to optimize content for SEO—word count, H2 keywords, keyword density, multimedia, tables, lists. Also use when the user mentions "content length," "word count," "keyword stuffing," "H2 keywords," "keyword density," "tables," "bullet points," or "content structure." For keywords, use keyword-research.

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When the user wants to set up, audit, or optimize analytics tracking (GA4, events, conversions). Also use when the user mentions "Google Analytics," "GA4," "event tracking," "conversions," "attribution model," "gtag," "data layer," "GA4 setup," "conversion tracking," "event setup," "User ID tracking," or "CTA attribution." For traffic insights, use traffic-analysis.

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Use when a task involves running a Scenario workflow through MCP, including anything the user calls a Scenario app, a saved pipeline, or a multi-step generation graph. Triggers include listing workflows, building workflow_run's inputs object, pricing a run with a dry run, approving or rejecting a stuck approval node, a run rejected for input length, or a workflows_list reply flooding the context. Creating or editing graphs is scenario-workflow-authoring. Keywords: workflow, app, approval gate.

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Use when generating or editing video with Luma Ray models on Scenario via MCP: cinematic text-to-video, image-to-video from a start frame, start plus end frame anchors, seamless looping clips, HDR output, restyling footage while preserving motion with edit strengths and face, pose, depth, or trajectory controls, reframing to another aspect ratio by outpainting, or budget prompt edits on real footage. Keywords: Luma, Dream Machine, Ray 3.2, Ray 3, Modify Video, Reframe, T2V, I2V, V2V, loop, HDR.

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Use when creating or editing music with ACE-Step models on Scenario via MCP: text-to-music songs with sung vocals from a lyric sheet, instrumental tracks, covering or restyling an existing song, repainting one section in place, changing sung lyrics, adding an instrument layer, completing a partial recording into a full arrangement, extracting stems, or choosing between Turbo and Quality lanes. Keywords: ACE-Step 1.5, cover strength, repaint, Vocal2BGM, stem separation, karaoke, BPM.

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Use when generating or editing images with Scenario through MCP: text-to-image, image-to-image, instruction editing, inpainting or outpainting with a mask, background control, aspect ratio or resolution sizing, several outputs per run, or choosing between Scenario image models. Also when a run fails on prompt length, a plan-restricted model, or a reference image that was silently ignored. Keywords: txt2img, img2img, image edit, inpaint, mask, reference image, aspect ratio.

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Use when generating or handling audio on Scenario via MCP. Triggers include music tracks, full-length songs with vocals written from lyrics, background scores, soundtracks, game sound effects, SFX, foley, ambience, looping audio, voiceover, narration, speech, TTS, text-to-speech, dialogue, voice cloning, re-voicing a recording, scoring or adding sound to a video, transcription, or requests to create, wait on, play, or download audio files (MP3, WAV) with Scenario tools.

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Patterns for individual long-form content pieces. Case studies, whitepapers, research reports, definitive guides, manifestos, ebooks, long-form tutorials. The structural disciplines that distinguish publication-quality long-form from bloggy-long padding or academic bloat. Different from pillar-content-architecture (which covers hub structure); this skill covers individual deep-dive pieces. Triggers on long-form content, case study writing, whitepaper, research report, definitive guide, ebook, manifesto, long-form tutorial, deep-dive article, anchor piece, foundational article, structural archetypes. Also triggers when a piece is over 3,000 words and the team is unsure how to structure it, when a long-form draft feels padded or saggy, or when a flagship asset needs the depth to actually earn the length.

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