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概要と使いどころ
Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.
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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.
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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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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.
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Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.
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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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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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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.
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Use this skill when the user asks how to build, measure, or improve safety culture in a motor carrier — leading vs lagging safety indicators, blame-free reporting, near-miss programs, safety committee structure, monthly safety meetings, ATA Safety Management Program guidance, and how to evaluate cultural maturity. Reference ATA SMP + DOT safety culture research.
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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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Backlink profile analysis: referring domains, anchor text distribution, toxic link detection, competitor gap analysis. Works with free APIs (Moz, Bing Webmaster, Common Crawl) and DataForSEO extension. Use when user says backlinks, link profile, referring domains, anchor text, toxic links, link gap, link building, disavow, or backlink audit.
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Maps intelligence for local SEO: geo-grid rank tracking, GBP profile auditing via API, review intelligence across Google/Tripadvisor/Trustpilot, cross-platform NAP verification, competitor radius mapping, and LocalBusiness schema generation. Three tiers: free (Overpass + Geoapify), DataForSEO, and DataForSEO + Google. Use when user says "maps", "geo-grid", "rank tracking", "GBP audit", "review velocity", "competitor radius", or "SoLV".
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Doctrine for all Supabase realtime: postgres_changes, broadcast, presence. Use before writing a `.channel(`/useChannel subscription, echo suppression, reconnect logic, an autosave loop beside realtime, or replacing polling with live updates, or when the tab freezes, messages duplicate, or a subscription delivers nothing.
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Run the full on-track check on a conversation, project, or keyword the owner names: find the sessions, extract exactly what he typed, dispatch independent judges who go to the live product as him and report what was missed, plan the remedy, and return one page — what he will see, what is missing, the plan. Use when told to check whether work is on track, to audit a project that has drifted, on 'run the on-track check on X', or when a long campaign is about to freeze, hand off, or claim done.
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One-route pattern: public marketing landing plus signed-in workspace. Use when creating or fixing a landing page or a feature's front door, guests see an error, 'make /X work signed out', signed-in users land on a pitch, or ModuleLanding / AuthedWorkspaceCTA. NOT for (public) share viewers or free tools.
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Elite frontend image-direction skill for generating premium, conversion-aware website design references. CRITICAL OUTPUT RULE — generate ONE separate horizontal image FOR EVERY section. A landing page with 8 sections produces 8 images. Never compress multiple sections into one image. Enforces composition variety (not always left-text / right-image), background-image freedom, varied CTAs, varied hero scales (giant / mid / mini minimalist), narrative concept spine, second-read moments, and a single consistent palette across all images. Optimized for landing pages, marketing sites, and product comps that developers or coding models can accurately recreate.
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Analyze and fix production errors from Sentry crash reports. Use when investigating AppHang, ANR, crashes, or production errors. Includes complete workflow from JSON analysis to bug fix implementation with evidence-based methodology. Triggers on sentry, crash, AppHang, ANR, error analysis, production error, bug analysis, crash report, freeze, hang, not responding, stacktrace, breadcrumbs, exception.
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A hard-edged writing style contract for timeless, forceful English prose without modern AI tics. Use when users ask for prose or rewrites that must be clean, exact, concrete, and free of AI cadence, filler, or therapeutic tone.
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Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.
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Auri: assistente de voz inteligente (Alexa + Claude claude-opus-4-20250805). Visao do produto, persona Vitoria Neural, stack AWS, modelo Free/Pro/Business/Enterprise, roadmap 4 fases, GTM, north star WAC e analise competitiva.
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Search and retrieve academic papers from arXiv using their free REST API. No API key needed. Search by keyword, author, category, or ID. Combine with web_extract or the ocr-and-documents skill to read full paper content.
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Spaced-repetition flashcard system. Create cards from facts or text, chat with flashcards using free-text answers graded by the agent, generate quizzes from YouTube transcripts, review due cards with adaptive scheduling, and export/import decks as CSV.
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Simple Preference Optimization for LLM alignment. Reference-free alternative to DPO with better performance (+6.4 points on AlpacaEval 2.0). No reference model needed, more efficient than DPO. Use for preference alignment when want simpler, faster training than DPO/PPO.
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Free web search via DuckDuckGo — text, news, images, videos. No API key needed. Prefer the `ddgs` CLI when installed; use the Python DDGS library only after verifying that `ddgs` is available in the current runtime.
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。