1,845 件 ・ 関連度順
概要と使いどころ
GitHub Actions security review for workflow exploitation vulnerabilities. Use when asked to "review GitHub Actions", "audit workflows", "check CI security", "GHA security", "workflow security review", or review .github/workflows/ for pwn requests, expression injection, credential theft, and supply chain attacks. Exploitation-focused with concrete PoC scenarios.
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Guides exploration of $autocapture events captured by posthog-js to understand user interactions, find CSS selectors (especially data-attr attributes), evaluate selector uniqueness, query matching clicks ad-hoc, and create actions. Use when the user asks about autocapture data, wants to find what users are clicking, needs to build actions from click events, asks about elements_chain, wants to build a trend or funnel filtered by clicks or other autocapture interactions, asks which properties autocapture sends, or asks how to filter $autocapture events. Only applies to projects using posthog-js autocapture.
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Reference for the Claude API / Anthropic SDK — model ids, pricing, params, streaming, tool use, MCP, agents, caching, token counting, model migration. TRIGGER — read BEFORE opening the target file; don't skip because it "looks like a one-liner" — whenever: the prompt names Claude/Anthropic in any form (Claude, Anthropic, Fable, Opus, Sonnet, Haiku, `anthropic`, `@anthropic-ai`, `claude-*`, `us.anthropic.*`, `[1m]`); the user asks about an LLM (pricing/model choice/limits/caching) — never answer from memory; OR the task is LLM-shaped with provider unstated (agent/MCP/tool-definition/multi-agent/RAG/LLM-judge/computer-use; generate/summarize/extract/classify/rewrite/converse over NL; debugging refusals/cutoffs/streaming/tool-calls/tokens). SKIP only when another provider is being worked on (overrides all triggers): OpenAI/GPT/Gemini/Llama/Mistral/Cohere/Ollama named in the query; OR `grep -rE 'openai|langchain_openai|google.generativeai|genai|mistralai|cohere|ollama'` over the project hits (run this grep FIRST if no provider named — don't Read the file).
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End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.
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Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks. Use when deciding bulk vs single-cell (bulk amplicon/RNA-seq -> MiXCR analyze preset -> VDJtools/immunarch depth-normalized diversity and overlap -> figures; 10x paired VDJ -> MiXCR 10x preset or Cell Ranger -> scirpy gene-expression integration, chain QC, clonotype clusters); and TCR vs BCR (TCR -> exact CDR3-nt+V/J clonotypes, VDJtools diversity is fine; BCR -> somatic hypermutation makes exact clonotypes wrong -> Immcantation distToNearest/findThreshold clonal clustering, germline reconstruction, SHM, Dowser lineages); selecting the MiXCR 4.x preset by chemistry and activating its license; downsampling to equal depth before comparing diversity or overlap; and optionally annotating antigen specificity.
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Chains a somatic (tumor-normal) SNV/indel and structural-variant pipeline end to end with GATK Mutect2 (or Strelka2), wiring the somatic-specific machinery - panel-of-normals and gnomAD germline-resource priors, GetPileupSummaries/CalculateContamination, and LearnReadOrientationModel FFPE/oxoG orientation-bias filtering fed into FilterMutectCalls. Use when calling somatic mutations from a tumor-normal pair (or tumor-only with PoN caveats), deciding which artifact filter removes which class of false positive, reasoning about VAF/purity/ploidy and clonal-vs-subclonal detection, adding somatic SV/CNV or TMB/MSI/signatures, or routing variants to AMP/ASCO/CAP tier and oncogenicity interpretation (never germline ACMG).
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Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, chaining QC/trim, BWA-MEM2 alignment, duplicate marking, optional BQSR, calling (bcftools/GATK HaplotypeCaller/DeepVariant/DRAGEN), normalization, site+genotype filtering, annotation, and hap.py/vcfeval benchmarking. Use when deciding the pipeline-wide reference-genome commitment (GRCh38 analysis set vs T2T, ALT/decoy handling), sequencing the steps in the defensible order (normalize BEFORE annotate, filter site- then genotype-level), choosing the calling engine and single-sample vs cohort joint-calling, picking a filtering strategy by cohort size, or benchmarking stratified within GIAB confident regions. Hands off mechanism to the variant-calling and read-alignment component skills; not a re-teach of any single step.
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End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/beta diversity at a declared sampling depth (phyloseq/vegan, adonis2 paired with betadisper), compositional DA as a consensus of >=2 tools (ALDEx2/ANCOM-BC2) on unrarefied counts, and optional PICRUSt2 functional prediction gated on NSTI. Covers the stage-ordering decisions (primers before truncation, per-run error model, rarefy for diversity not DA, predicted potential not activity) and defers each per-step choice to the six microbiome skills. Use when staging an amplicon study end to end or chaining ASV inference, taxonomy, diversity, and differential abundance. For shotgun reads see workflows/metagenomics-pipeline.
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End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations. Orchestrates the read -> compensate/unmix -> transform -> QC -> doublet-removal -> cluster-or-gate -> annotate -> diffcyt DA/DS chain with flowCore/CATALYST/diffcyt, branching on instrument type and on clustering-vs-gating. Use when processing a cytometry experiment end-to-end, deciding the pipeline path for an instrument, or wiring the flow-cytometry component skills into one analysis with valid sample-level statistics.
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End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.
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Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari benchmarking - chaining ONT and PacBio HiFi runs while handing the SV signal mechanism off to the component skills. Use when running a long-read SV workflow from reads to a benchmarked callset, choosing the minimap2 preset and SV caller by platform and goal, deciding when long reads are worth it for the insertions and repeat-mediated SVs short reads physically miss, building a joint-genotyped cohort with the two-step .snf design, or parameterizing a Truvari benchmark against GIAB HG002 Tier 1 plus CMRG. Not for the SV signal mechanism itself (see variant-calling/structural-variant-calling) or short-read SV.
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Agentic and machine-to-machine payments on Stellar. Covers x402 (HTTP 402 paid APIs via OZ Channels facilitator, fee-sponsored clients) and MPP (Machine Payments Protocol) in both Charge mode (per-request SAC) and Channel mode (off-chain commits, high-frequency). Defaults to USDC (SEP-41 SAC) on `stellar:testnet`/`stellar:pubnet` (CAIP-2). Use when selling a paid API to AI agents, building an x402 client, or designing a payment-channel architecture for high-frequency agent traffic.
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Querying Stellar chain data via Stellar RPC (preferred) and Horizon (legacy). Covers RPC JSON-RPC methods, Horizon REST endpoints, streaming, pagination, historical queries, Hubble/Galexie for deep history, and the RPC/Horizon migration story. Use when reading balances, transactions, operations, ledgers, contract events, or building any indexer/analytics workflow.
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Roslyn-powered semantic query CLI for C# solutions. Use when you need to find references, callers, implementations, dependencies, members, or trace call chains in a C# codebase — replaces multi-round grep/read cycles with single precise queries.
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Integrate Iteration Layer APIs for document, website, image, and sheet processing. Composable APIs — Document Extraction, Website Extraction, Document to Markdown, Image Transformation, Image Generation, Document Generation, and Sheet Generation — share one credit pool and chain together into workflows.
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Harden LLM and agent integrations you operate: prompt injection, tool allowlists, secret leakage, and supply-chain of models. Defensive only.
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Cut a release of the Lyrion Dashboard. Use this whenever a task is about shipping a new version — bumping the version, tagging, the Release workflow, or how the Android APK and the Docker image get built and published. Covers the single source of truth for the version, the manual `Release` → publish → `android.yml` + `docker.yml` chain, the versionCode packing, and the F-Droid constraint that keeps versions static in source. Reach for it before touching `VERSION`, `release.yml`, or the Android `versionName`/`versionCode`.
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Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca (Illumina, repeat-aware), Pilon (legacy short-read), NextPolish/NextPolish2, Hapo-G (haplotype-aware), ntEdit, and DeepPolisher/PEPPER-Margin-DeepVariant for human. Covers the do-not-polish-HiFi rule, the medaka basecaller-model footgun, held-out Merqury QV as the only honest stop signal, and the haplotype-collapse trap. Use when correcting homopolymer indels or residual SNPs in a long-read assembly, deciding if a HiFi assembly needs polishing, or choosing an ONT vs hybrid vs short-read polishing chain.
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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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Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.
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Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.
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Build natural-language crypto/DeFi agents and EVM MCP plugins (Claude Code, Cursor, Codex, Gemini). Aomi turns prompts into wallet-signed txs on Ethereum, Base, Arbitrum, Optimism, Polygon, Linea — non-custodial, fork-simulated. 40+ apps: Uniswap, Aave, Lido, Morpho, GMX, Hyperliquid, Polymarket.
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Cross-company language sweep via Quartr full-text search — date the adoption curve of a term/phrase across the global transcript+filing corpus, identify which companies (and which speaker roles) use it and when they started, and cross-reference against vault theses and graph adjacency to flag terms propagating through supply chains the book owns. Use when user says "sweep", "who is talking about X", "language scan", "adoption curve for X", or "is X inflecting".
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Supply chain investigation, evidence recovery, and forensic analysis for GitHub repositories. Covers deleted commit recovery, force-push detection, IOC extraction, multi-source evidence collection, hypothesis formation/validation, and structured forensic reporting. Inspired by RAPTOR's 1800+ line OSS Forensics system.
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。