「ada」の検索結果

Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences. Use when scoring a gene's codon bias against a host, optimizing a CDS for heterologous expression, or studying synonymous codon selection.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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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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Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submissions or precision-medicine claims.

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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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Implement authentication and authorization with Better Auth - a framework-agnostic TypeScript authentication framework. Features include email/password authentication with verification, OAuth providers (Google, GitHub, Discord, etc.), two-factor authentication (TOTP, SMS), passkeys/WebAuthn support, session management, role-based access control (RBAC), rate limiting, and database adapters. Use when adding authentication to applications, implementing OAuth flows, setting up 2FA/MFA, managing user sessions, configuring authorization rules, or building secure authentication systems for web applications.

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Search scientific papers via the BGPT MCP server and retrieve structured experimental data — methods, results, conclusions, quality scores, and 25+ metadata fields per paper.

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Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.

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Propose the next dependency-ready sprint from the ALREADY-DECOMPOSED roadmap — standup's active sibling. Reads docs/roadmap-execution-plan.md + the memory backlog, computes per-task readiness from the roadmap's machine-readable status, orders with roadmap-planner's graph engine, and emits a proposed task-set (sprint-plan manifest shape) with per-feature done-criteria, excluding unready tasks and naming their unmet prerequisite. PROPOSES ONLY — the human confirms/edits before /triage routes it (typically to the `power` track). Distinct from `sprint-plan`, which decomposes a fresh vision.

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Draft or revise English prose for any brief — documentation body, intake problem statements, spec context, RCA summaries, marketing copy, README sections, PR descriptions. Mandatorily invokes `Skill(humanizer)` as the final pass on every draft. Conditionally invokes `copywriting` for persuasive register, `documentation` for reference docs, `technical-tutorials` for tutorials. Used when any phase needs human-readable prose written or rewritten. Composition only — research and register-picking happen in the caller's context.

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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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Use when you need a minimal example skill to copy or test the toolkit.

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。

Provide comprehensive techniques for penetration testing AWS cloud environments. Covers IAM enumeration, privilege escalation, SSRF to metadata endpoint, S3 bucket exploitation, Lambda code extraction, and persistence techniques for red team operations.

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Audits and designs iOS/macOS/watchOS/visionOS interfaces against the Apple Human Interface Guidelines, including the Liquid Glass design language (announced WWDC25, shipped with iOS 26/macOS Tahoe, Sept 2025). Use when reviewing an Apple-platform mockup or app for HIG compliance, checking contrast or tap-target sizes, or designing native-feeling Apple UI (e.g., 'audit my iOS app against the HIG', 'is this text readable on Liquid Glass?').

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Geracao de imagens humanizadas via Google AI Studio (Gemini). Fotos realistas estilo influencer ou educacional com iluminacao natural e imperfeicoes sutis.

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Practical UI refactoring and visual design review inspired by Refactoring UI by Steve Schoger and Adam Wathan. Use when an AI coding agent needs to improve an existing interface, audit visual polish, redesign a rough UI, review frontend code for hierarchy/spacing/typography/color/depth/image issues, or turn a plain implementation into a cleaner product-quality screen. Do not use for creating UI from scratch, scaffolding a new app, building a new landing page, or designing a new design system unless the user explicitly asks to review or refactor an existing interface.

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Skill for building with the Astro web framework. Helps create Astro components and pages, configure SSR adapters, set up content collections, deploy static sites, and manage project structure and CLI commands. Use when the user needs to work with Astro, mentions .astro files, asks about static site generation (SSG), islands architecture, content collections, or deploying an Astro project.

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Compress natural language memory files (CLAUDE.md, todos, preferences) into caveman format to save input tokens. Preserves all technical substance, code, URLs, and structure. Compressed version overwrites the original file. Human-readable backup saved as FILE.original.md. Trigger: /caveman:compress <filepath> or "compress memory file"

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。

Compress natural language memory files (CLAUDE.md, todos, preferences) into caveman format to save input tokens. Preserves all technical substance, code, URLs, and structure. Compressed version overwrites the original file. Human-readable backup saved as FILE.original.md. Trigger: /caveman:compress <filepath> or "compress memory file"

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Use when male Chinese web novel writing or 男频小说写作 needs contemporary Chinese 热梗, 网络流行语, 轻笑话, 网络热门事件模板, 网络热门人物口头禅, 知名人物事件的安全化改写或模仿, 弹幕, 评论区, 角色对白, 短视频文案, Fanqie male-rank market radar, or work-study notes on writing style, characters, background, outline, and themes for AI-assisted fiction writing.

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Summarizes uncommitted git changes in a concise machine-readable format. Use in CI pipelines, scripts, or headless invocations where the output will be piped or captured.

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Review code against a standard checklist covering security, correctness, performance, and readability. Use when asked to review code, check a PR, or audit changes.

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Re-run the analysis pipeline on all runs matching an RQ, reaggregate metrics, and propose findings updates against the fresh data. Trigger when the user says "reanalyze RQ-N", "reanalyse RQ-N", "Runs neu analysieren", or wants to refresh metrics/findings after a pipeline change (analyze-run.sh fix, adapter added, ESLint config).

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。