“toc”的搜索结果

Claude Code (code.claude.com) デプロイ・CI/CD リファレンス。 Amazon Bedrock / Google Cloud Agent Platform (Vertex AI) / Microsoft Foundry / Claude Platform on AWS、 Claude apps gateway、LLM gateway (protocol / rollout)、 GitHub Actions (claude-code-action) / GitLab CI/CD / GitHub Enterprise Server (GHES)、 Code Review (REVIEW.md・review level・@claude review always・コスト・トラブルシュート)、 ローカル /code-review、ultrareview (claude ultrareview)、 Slack (Claude Tag、旧 Claude Code in Slack、Pro/Max)、 headless mode、cloud environments、devcontainer、 self-hosted environments（runner 構成・identity 検証・本番デプロイ）。

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Ark UI headless / unstyled コンポーネントライブラリ。Zag.js ベース、Chakra UI v3 基盤。 React / Solid / Vue / Svelte 対応。asChild, RootProvider, createListCollection, createTreeCollection, Presence hideMode, useHotkey / useHotkeys, data-* セレクタ。 Navigation Menu, TOC, Tour, Signature Pad, Image Cropper, Floating Panel, Angle Slider 等のコンポーネント API。

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Blender Python API リファレンス。bpy / bmesh / mathutils / gpu / bpy_extras モジュール、 bpy.data / bpy.context / bpy.ops / bpy.types / bpy.props / bpy.msgbus / bpy.path コア API。 Mesh / Modifier / Geometry Nodes / Armature / Keyframe / Driver / Shape Key / NLA、 Cycles / EEVEE / Shader Nodes / Rigid Body / Cloth / Fluid / Compositor Nodes / AOV、 headless CLI レンダリング、add-on 開発、Extensions システム、MCP Server (Model Context Protocol)。

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Analyze binaries or protocols you own (or have license to inspect) to improve security, compatibility, or incident response. Not for cracking, DRM bypass, or malware creation.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 7.

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

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Use when building MCP (Model Context Protocol) servers in Java/Spring Boot. Covers tool registration, resource exposure, prompt templates, and production deployment using the official MCP Java SDK. Use when user mentions MCP, AI agent integration, or tool calling.

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Build production-ready Web3 applications, smart contracts, and decentralized systems. Implements DeFi protocols, NFT platforms, DAOs, and enterprise blockchain integrations.

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Built-in MCP (Model Context Protocol) client that connects to external MCP servers, discovers their tools, and registers them as native Hermes Agent tools. Supports stdio and HTTP transports with automatic reconnection, security filtering, and zero-config tool injection.

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图片主导的社交卡 — 图是证据 / 氛围 / 产品 / 物件 / 地点 / 钩子，文字让位。骨架：全出血 + 安全标题块 / 大图井 + 编辑标题 / 图片裁切 + caption 账本 / 产品物件照 + 三个证据点 / 旅行地点 + 地图或位置元数据。必须保护人脸 / 产品 / UI / 关键细节不被文字盖住。触发："做个图片卡 / 照片封面 / 产品图卡 / 旅行卡 / 物件卡 / 证据图卡"。NOT 没图片只能补 stock 装饰，NOT 用蒙版强行救烂图。

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Review or refactor an existing SKILL.md and its bundled resources — a smaller always-loaded core, conditional references, preserved behavior, lean/guided consumer profiles, and an A/B protocol to compare a candidate with the previous version. Use when a skill repeats itself, loads references on every run, triggers too broadly or misses legitimate requests, or needs its efficiency measured across models. Do NOT use for writing a new skill from scratch, refactoring application code, translating a skill verbatim, or performing the target skill's own task.

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Build Model Context Protocol (MCP) servers and tools that extend Claude's capabilities with custom functions, data sources, and integrations. Use when creating custom MCP servers, implementing tools for Claude, building integrations with external services, creating data source connectors, implementing custom functions, or extending Claude's capabilities with domain-specific tools.

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Genera o actualiza una especificación SDD (spec.md) para HagamosTech. Úsala cuando haya que definir una nueva funcionalidad o vertical antes de tocar código, entrevistando al usuario y produciendo requisitos funcionales en notación EARS. Trigger: crear/actualizar spec, nuevo requisito, /spec.

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Turn any markdown file into a publication-quality PDF. Proper 1in margins, intelligent page breaks, page numbers, cover pages, running headers, curly quotes and em dashes, clickable TOC, diagonal DRAFT watermark. Not a draft artifact — a finished artifact. Use when asked to "make a PDF", "export to PDF", "turn this markdown into a PDF", or "generate a document". (gstack) Voice triggers (speech-to-text aliases): "make this a pdf", "make it a pdf", "export to pdf", "turn this into a pdf", "turn this markdown into a pdf", "generate a pdf", "make a pdf from", "pdf this markdown".

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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Write or revise AI-learning-notes article pages in "寫文章模式" when the user asks for articles, technical articles, blog posts, bilingual versions, article formatting consistency, shared article-base alignment, responsive layout, summary/TOC decisions, contrast, or publishing-flow compatibility.

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