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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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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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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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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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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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Use this skill for training drivers on effective pre-trip inspection technique. Covers the comprehensive walk-around, time investment, and common areas drivers miss.

日本語の概要は準備中です。原文の説明を表示しています。

Use this skill when the user asks about driver fatigue management — circadian rhythm impact on driving, recognizing fatigue, fatigue risk management programs (FRMS), night driving safety, microsleep recognition, drowsiness detection technology, and how HOS rules relate to actual fatigue (and why 11-hour driving is risky even when legal). Reference FMCSA Fatigue Management research.

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Use this skill when the user asks about driver ergonomics — back/neck/shoulder injury prevention, seat adjustment + lumbar support, entering and exiting cab safely, load handling techniques, vibration reduction, stretching protocols, and how ergonomics affects workers compensation costs in trucking. Reference OSHA + ATA ergonomics research.

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Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

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Deep single-page SEO analysis covering on-page elements, content quality, technical meta tags, schema, images, and performance. Use when user says "analyze this page", "check page SEO", "single URL", "check this page", "page analysis", or provides a single URL for review.

日本語の概要は準備中です。原文の説明を表示しています。

When the user wants to audit, review, or diagnose SEO issues on their site. Also use when the user mentions "SEO audit," "technical SEO," "why am I not ranking," "SEO issues," "on-page SEO," "meta tags review," or "SEO health check." For building pages at scale to target keywords, see programmatic-seo. For adding structured data, see schema-markup.

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Automatically creates user-facing changelogs from git commits by analyzing history, categorizing changes, and transforming technical entries into customer-friendly release notes. Use when preparing release notes from commit logs.

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Generate blog articles for Qiita and Zenn from GitHub release information. Use when creating release notes or technical articles that follow specific markdown formats with frontmatter. Supports generating articles from release data, creating custom formatted articles, and saving articles to specified repositories for both Qiita and Zenn platforms

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Pushes interfaces past conventional limits with technically ambitious implementations — shaders, spring physics, scroll-driven reveals, 60fps animations. Use when the user wants to wow, impress, go all-out, or make something that feels extraordinary.

日本語の概要は準備中です。原文の説明を表示しています。

Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

日本語の概要は準備中です。原文の説明を表示しています。

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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Pull version-current Convex docs for the version this project uses — pin the installed version, fetch page-as-markdown or check node_modules types, freshness hierarchy — instead of writing a possibly-stale API from memory.

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Expert writing for technical content, social media, and developer documentation. Use when asked to write tweets, LinkedIn posts, blog posts, READMEs, commit messages, feature announcements, or any written content. Optimized to avoid AI detection patterns.

日本語の概要は準備中です。原文の説明を表示しています。

Documentation knowledge base. Provides documentation types, audiences, best practices, and antipatterns for technical documentation creation.

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Generates Mermaid diagrams for technical documentation. Provides templates for flowcharts, sequence diagrams, class diagrams, ER diagrams, and C4 models.

日本語の概要は準備中です。原文の説明を表示しています。

Diagram knowledge base. Provides Mermaid syntax, C4 model, diagram types, and best practices for technical diagrams.

日本語の概要は準備中です。原文の説明を表示しています。

Write academic research documents following academic guidelines with peer-reviewed sources from Google Scholar and other academic databases. Always verify source credibility and generate IEEE standard references. Use for research papers, literature reviews, technical reports, theses, dissertations, conference papers, and academic proposals requiring proper citations and scholarly rigor.

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Toolkit for creating an entertainingly stupid README that manages to give off Tim & Eric, Steve Brule vibes while maintaining a level of technical acumen that is expected of a modern open source project. This skill applies when users request a silly or absurd README.

日本語の概要は準備中です。原文の説明を表示しています。