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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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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/SQANTI-LR (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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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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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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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Use this skill to evaluate which defensive driving program is best for your fleet. Compares Smith System, CarriersEdge, Compass-native training, and other options.

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Use this skill to understand FMCSA hearing standards for CMV drivers. Covers the forced whisper test, audiometry alternative, and certification for hearing-impaired drivers.

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Multi-page Lighthouse audit via the MIT-licensed Unlighthouse CLI. Free-tier alternative to running PageSpeed against every URL on a site, no API quota burn, runs locally.

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iOS-native mobile web UX rules. Use when building any UI component, fixing mobile issues, reviewing responsive code, or touching viewport heights (dvh vs h-screen), safe areas, Dialog vs Drawer, tabs on mobile, touch targets, or input zoom.

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Analyze an idea, proposal, change, claim, or decision from facts through problem, value, mechanism, consequences, evidence, alternatives, and action. Use when the user asks what something is for, why it matters, whether it is worth doing, what impact it has, or how to decide. Do not use for simple factual lookup or straightforward execution.

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Elite mobile app image-generation skill for creating premium, app-native screen concepts and flows. Designed for iOS, Android, and cross-platform mobile products. Prioritizes clean hierarchy, comfortably readable text, strong multi-screen consistency, controlled color palettes, non-generic creative direction, textured surfaces, image-led composition, tasteful custom iconography, and clean phone mockup framing. By default, screens should be shown inside a subtle premium iPhone or similar phone mockup with a visible frame, while the main focus stays on the app content itself. This skill generates images only. It does not write code.

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Action-Domain-Responder pattern knowledge base. Provides patterns, antipatterns, and PHP-specific guidelines for ADR (web-specific MVC alternative) audits.

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Transparent, rigorous research with full methodology — not a black-box API wrapper. Conducts exhaustive investigation through mandated 2-cycle research per theme, APA 7th citations, evidence hierarchy, and 3 user checkpoints. Self-contained using native OpenClaw tools (web_search, web_fetch, sessions_spawn). Use for literature reviews, competitive intelligence, or any research requiring academic rigor and reproducibility.

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Date and time formatting for OneKey applications. Use when displaying dates, timestamps, or formatting time in UI components. Always use OneKey utilities instead of native JS date methods. Triggers on date, time, timestamp, formatDate, formatTime, toLocaleDateString, toLocaleString, dateUtils, locale, format, display date, show time, datetime, calendar.

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Performance optimization guidelines for OneKey React/React Native applications. Use when optimizing app performance, fixing UI freezes/lag, reducing re-renders, handling concurrent operations, or analyzing performance bottlenecks. Triggers on performance, optimization, optimize, slow, lag, freeze, hang, jank, stutter, memory, leak, concurrent, batching, batch, memoization, memo, bridge, windowSize, contentVisibility, FlashList, re-render, fps, tti, bundle.

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Perform 12-Factor App compliance analysis on any codebase. Use when evaluating application architecture, auditing SaaS applications, or reviewing cloud-native applications against the original 12-Factor methodology.

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X/Twitter API integration for posting tweets, threads, reading timelines, search, and analytics. Covers OAuth auth patterns, rate limits, and platform-native content posting. Use when the user wants to interact with X programmatically.

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Create platform-native content systems for X, LinkedIn, TikTok, YouTube, newsletters, and repurposed multi-platform campaigns. Use when the user wants social posts, threads, scripts, content calendars, or one source asset adapted cleanly across platforms.

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Design spec with 98 rules for building CLI tools that AI agents can safely use. Covers structured JSON output, error handling, input contracts, safety guardrails, exit codes, and agent self-description.

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Convert human-written CLAUDE.md into AI-native structured-label format. Battle-tested across 4 models. Same rules, fewer tokens, higher compliance.

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Prefer native 1c-publish-http. Публикация информационной базы 1С через…

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Prefer native 1c-update-db. Обновление конфигурации базы данных 1С. Исп…

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Prefer native 1c-load-diff-src, 1c-load-task-src. Загрузка изменений из…

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