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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV and AnnotSV for semi-automated scoring. Covers the separate copy-number-loss and copy-number-gain rubrics, the five-tier classification, ClinGen haploinsufficiency/triplosensitivity and dosage-sensitive regions, de novo and segregation evidence, and population-frequency benign evidence. Use when assigning pathogenic/likely-pathogenic/VUS/likely-benign/benign to a constitutional CNV, scoring a CNV against ACMG/ClinGen criteria, or distinguishing the automatable evidence from the case-specific evidence requiring manual input.

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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA 2023 covariate adjustment guidance. Covers Table 1 generation, analysis populations (ITT/FAS/PP/Safety), the 5 ICH E9(R1) intercurrent-event strategies, MMRM under MAR (mmrm), reference-based MI (rbmi J2R/CR/CIR), Permutt tipping-point sensitivity, and Rubin's-rules vs frequentist variance debate. Use when preparing regulatory submissions, defining estimands, or implementing missing-data sensitivity analyses.

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Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiotropy and choosing among Egger, MR-PRESSO, MR-RAPS, CAUSE, LHC-MR, LCV, MR-Clust, MR-Mix, and contamination-mixture methods. Use when validating an MR causal claim, running the STROBE-MR sensitivity battery, suspecting a shared heritable confounder, working under weak-instrument or polygenic-exposure regimes, or reconciling discordant estimates across robust methods.

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Create and manage database migrations with reversible changes, proper naming conventions, and zero-downtime deployment strategies. Use this skill when creating database migration files, modifying schema, adding or removing tables/columns, managing indexes, or handling data migrations. Apply when working with migration files (e.g., db/migrate/, migrations/, alembic/, sequelize migrations), schema changes, database versioning, rollback implementations, or when you need to ensure backwards compatibility during deployments. Use for any task involving database structure changes, index creation, constraint modifications, or data transformation scripts.

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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Define database models with clear naming, appropriate data types, constraints, relationships, and validation at multiple layers. Use this skill when creating or modifying database model files, ORM classes, schema definitions, or data model relationships. Apply when working with model files (e.g., models.py, models/, ActiveRecord classes, Prisma schema, Sequelize models), defining table structures, setting up foreign keys and relationships, configuring cascade behaviors, implementing model validations, adding timestamps, or working with database constraints (NOT NULL, UNIQUE, foreign keys). Use for any task involving data integrity enforcement, relationship definitions, or model-level data validation.

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Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include "method validation", "analytical method validation", "AMV", "validation protocol", "acceptance criteria", "linearity", "reportable range", "accuracy and precision", "repeatability", "intermediate precision", "recovery", "LOD", "LOQ", "detection limit", "quantitation limit", "specificity", "robustness", "method transfer", "method comparison", "Deming", "Passing-Bablok", "Bland-Altman", "equivalence testing", "OOS investigation", "ICH Q2", "Q2(R2)", "Q14", "USP 1225", "ICH M10", "incurred sample reanalysis", "ISR", "CLSI EP", and any request to show that an assay works.

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Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.

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Process and generate multimedia content using Google Gemini API. Capabilities include analyze audio files (transcription with timestamps, summarization, speech understanding, music/sound analysis up to 9.5 hours), understand images (captioning, object detection, OCR, visual Q&A, segmentation), process videos (scene detection, Q&A, temporal analysis, YouTube URLs, up to 6 hours), extract from documents (PDF tables, forms, charts, diagrams, multi-page), generate images (text-to-image, editing, composition, refinement). Use when working with audio/video files, analyzing images or screenshots, processing PDF documents, extracting structured data from media, creating images from text prompts, or implementing multimodal AI features. Supports multiple models (Gemini 2.5/2.0) with context windows up to 2M tokens.

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This skill determines whether inpatient diabetic patients meet high-risk criteria for CGM initiation using Table 3 factors such as age ≥65 years, BMI ≤27 kg/m², type 1 diabetes, insulin regimen, and specific clinical conditions. It is triggered by clinician questions like "Should I assess this inpatient for CGM initiation based on hypoglycemia risk?" or "Is this patient a candidate for inpatient CGM?"

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Suggests initiating inpatient CGM for select diabetic patients at high risk for hypoglycemia based on Table 3 criteria. Triggers include "Should I initiate CGM for this hospitalized diabetic patient at high risk for hypoglycemia?" or "Is inpatient CGM warranted for this patient?"

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Apply the four published expert-consensus clinical scenarios to manage GI adverse events in complex GLP-1 receptor agonist patients — persistent nausea mid-titration, GERD/heartburn after up-titration, elderly with sarcopenia risk, and insulin-treated elderly with CKD plus diarrhoea. Use when a clinician describes a patient resembling one of these archetypes, or asks "how to manage GLP-1 in an elderly patient with CKD", "patient on liraglutide developed reflux", "sarcopenia worry on semaglutide in 80-year-old", or "persistent nausea on semaglutide despite escalation". Grounded in Gorgojo-Martínez 2023 Table 4.

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This skill recommends measuring serum cortisol or urine free cortisol off-medication at 6- to 12-month intervals to assess radiation therapy effect in patients with Cushing's syndrome undergoing or post-radiotherapy. It is also indicated when patients on stable medical therapy develop new adrenal insufficiency symptoms such as fatigue, weight loss, or hypotension.

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Provides guidance on acceptable blood sampling conditions for primary aldosteronism screening when ideal early‑morning supine fasting conditions cannot be met. Triggers include when a clinician says “The patient wasn’t fasting/supine” or questions whether non‑ideal sampling affects screening validity.

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This skill determines whether confirmatory testing can be omitted after a positive aldosterone-to-renin ratio (ARR) in patients with suspected primary aldosteronism. It is applied when a patient exhibits spontaneous hypokalemia, undetectable renin, and a plasma aldosterone concentration ≥20 ng/dL (550 pmol/L).

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Determines follow‑up interval for patients with primary adrenal insufficiency (PAI) based on age: annual visits for adults and children, and every 3–4 months for infants. Triggered when establishing routine endocrine care after PAI diagnosis or during stable management.

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Teaches AI patients about stress-dosing and emergency glucocorticoid administration; instructs to obtain emergency card/bracelet/necklace and kit with injectable high-dose GC. Triggers when counseling any patient with adrenal insufficiency (e.g., "Use when counseling patient with adrenal insufficiency...").

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Draft a Workflow Phase 1 intake document capturing a new request — the problem, the desired outcome, constraints, and testable acceptance criteria. Use when a user brings a new feature, change, or investigation that doesn't yet have a spec. The output lives at `docs/intake/<slug>.md` and feeds `/scout`, `/research`, and `/spec` downstream.

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Write executable failing tests from a recipe handed to you by the main context. Used by `/tdd` Step 2 and ad-hoc when a phase needs tests-first to drive implementation. Decisions about which scenarios to cover, which categories matter, and which fixtures to use are made by the caller — this skill executes that recipe with code-structure discipline.

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Drift check between the baseline implementation on disk and the claims in `docs/init/seed.md` + cross-references in CLAUDE.md, README.md, and the rendered docs site. Verifies hook/agent/skill/command names + counts, settings.json wiring, project.json key presence, .mcp.json servers, vendored license files, and helper script presence. Exit 0 PASS / 1 FAIL — suitable for CI. Read-only; safe to invoke any time.

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Preflight a spec draft without saving. Runs the same checks as the write-boundary hooks — PlantUML syntax, required diagram presence, AC-to-sequence traceability, Design calls quality floor, and System delta row resolution — and prints a compact pass/fail table. Use while iterating so the hooks don't bite on save.

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An infographic skill for AI agents — works inside Claude Code, Codex, Hermes, OpenClaw, Cursor, and any agent host that loads skills. Create professional infographics as self-contained HTML files with PNG exports. Use when the user asks to create, design, generate, build, or make an infographic, data visualization, visual explainer, chart poster, cheatsheet, or pocket guide. Trigger phrases include "make this visual", "turn this into a graphic", "visualize this data", "infographic for X", "cheatsheet for X", or when the user provides structured data (tokenomics allocations, ecosystem/partner lists, timelines, comparisons, step-by-step processes) AND asks for a visual output. Covers tokenomics, ecosystem overviews, game overviews, cheatsheets, airdrop guides, comparisons, and process flows. Do NOT trigger for plain text answers, markdown tables, bulleted summaries, questions asking for advice or explanations about a topic (even when the topic is tokenomics, ecosystem, vesting, etc.), inline chat diagrams, or data processing with no visual output requested. The signal is "asks for a visual", not "mentions a keyword".

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