「oss」の検索結果

process fixture의 cross-worker failover는 opt-in 명시 필요

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Cross-stack security review — auditing vulnerabilities across infrastructure, smart contracts, CI/CD pipelines, and AI agent systems, plus auth/sessions/crypto and validating user input at API and infrastructure boundaries. Triggers on mentions of "vulnerability", "pentest", "OWASP", "access control", "injection", "CSRF", "JWT", "smart contract audit", "supply chain", "OIDC", or any review of security-sensitive code paths spanning more than one layer. For PII sanitization see [security](../security/SKILL.md).

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Maintain SESSION-STATE.md, the durable within-session memory that survives context compaction. Use when a constraint, settled decision, existing-infrastructure (survey) finding, or open thread must persist across a long session so it is not re-derived or re-litigated. Triggers on /state, "remember this for the session", "record this constraint/decision", or after surveying what already exists. For cross-session/personal memory use .claude/memory/ on Claude or native memories on Codex; for repo-derivable facts, do not record at all.

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Extract a DDD-style ubiquitous language glossary from the current conversation, flagging ambiguities and proposing canonical terms. Saves to UBIQUITOUS_LANGUAGE.md. Use when user wants to define domain terms, build a glossary, harden terminology, create a ubiquitous language, or mentions "domain model" or "DDD".

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Align, run, audit, and publish GEODE benchmark comparisons against Agent-World arXiv 2604.18292v1 across MCP-Mark, BFCL V4, and tau2-bench. Use for Agent-World or AgentWorld comparison requests, cross-suite agent benchmark design, Tau2 comparator/profile diagnosis, paired thin-runtime-versus-GEODE experiments, mean-accuracy@8 replication, or benchmark comparability and artifact reviews.

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Resume an interrupted orchestration run across Claude Code sessions using MANIFEST.yaml

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Generates a cross-referenced U.S. nonprofit annual filing package for state charity-bureau registration. Produces Full Compliance Package, Form-Field Mode, or Executive Briefing with source citations, disclosure cross-checks, and filing instructions. Trigger when the user drafts annual report submissions, renewal packets, penalty-of-perjury certifications, or charity bureau filings. Also trigger on Form RRF-1, CHAR500, BCO-10, nonprofit annual report, charity registration renewal, or fundraiser disclosure attachments.

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Compassionate bereavement support, memorial creation, grief education, and healing journey guidance. Specializes in understanding grief stages, creating meaningful tributes, and supporting the non-linear path of loss.

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Use when designing matrix builds (OS x version x dimension), composing reusable workflows, gating jobs on conditions, doing OIDC to AWS/GCP/Cloudflare without long-lived secrets, sharding tests across runners, or fixing cache invalidation. Triggers: workflow_call between repos, fail-fast: false tradeoffs, exclude/include matrix surgery, environment protection rules, OIDC trust policy setup, concurrency cancellation on duplicate pushes, artifact reuse across jobs, conditional job matrices computed at runtime. NOT for GitLab CI / CircleCI / Jenkins (different yaml dialects), self-hosted runner administration, or local act dev.

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Long-running design anthropologist that builds comprehensive visual databases from 500-1000 real-world examples, extracting color palettes, typography patterns, layout systems, and interaction design across any domain (portfolios, e-commerce, SaaS, adult content, technical showcases). This skill should be used when users need exhaustive design research, pattern recognition across large example sets, or systematic visual analysis for competitive positioning.

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Tracks cumulative LLM costs across DAG execution and makes real-time decisions to stay within budget. Downgrades models, skips optional nodes, or stops early when cost exceeds thresholds. Use when managing execution budgets, analyzing cost breakdowns, or optimizing model routing for cost. Activate on "cost budget", "too expensive", "reduce cost", "cost optimization", "model downgrade", "budget exceeded". NOT for LLM model selection logic (use llm-router), pricing comparisons across providers, or billing/invoicing.

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Use when stuck on approach (not debugging). Strategic unsticking via 7 non-default techniques: simplification cascades, collision-zone thinking, meta-pattern recognition, inversion, scale game, first principles, via negativa. Triggers on complexity spiraling, innovation block, recurring patterns across domains, forced-assumption solutions, scale uncertainty, told-it's-impossible, or bloated systems needing subtraction. For evidence-based root-cause debugging, use mk:sequential-thinking instead.

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Use when writing or reviewing Go code in fusionaly-oss — adding routes, handlers, domain contexts, background jobs, the manager CLI, wiring the app, or writing tests. Covers the cartridge framework, matcha for the manager, Phoenix Contexts, lifecycle/shutdown, and the test conventions.

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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody methods cannot resolve, and orthogonal validation (miCLIP/GLORI/m6A-SAC-seq/m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set, reconciling differing peak sets across tools, validating MeRIP peaks against single-base methods, interpreting 5' peaks where m6Am contamination is possible, or recommending a consensus strategy.

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Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof, premessa), and reference-anchor cross-batch normalization (CytoNorm, per-cluster quantile splines). Covers the distinction between within-run drift correction and between-batch correction, the mandatory anchor/reference sample, why normalization is per-cluster with many quantiles, and the over-correction risk. Use when correcting CyTOF signal drift, harmonizing multi-batch or multi-site studies, or deciding whether to normalize data versus model batch in the design.

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Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA log-fold-change as the product of a treatment-dependent gene-essentiality term and a treatment-independent guide-efficacy term. Covers the Bayesian decomposition math, the hierarchical efficacy prior shared across screens performed with the same library, when JACKS outperforms MAGeCK (multi-screen joint analysis, libraries with broad efficacy variance) and when it does not (single screen, novel libraries with no prior efficacy), library-reuse efficacy transfer, downstream essentiality interpretation, and the 2.5x sample-size reduction enabled by efficacy-aware testing. Use when running multiple screens with the same library, when guide-level noise is suspected to dominate per-gene signal, when reusing published essentiality reference screens for efficacy priors, or when comparing screens performed across cell lines that share library but differ biologically.

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Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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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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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers between conditions, identifying master transcription factor networks, or predicting BET-inhibitor responsiveness.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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。