「ept」の検索結果

Use when you need to design, review, or improve security in Micronaut applications — including micronaut-security authentication, @Secured and intercept-url-map rules, JWT/session strategies, SecurityService checks, CORS, CSRF awareness for browser apps, rejection handlers, and sensitive-data-safe logging. This should trigger for requests such as Add Micronaut security support; Review Micronaut security configuration; Improve API authorization in Micronaut; Add JWT security in Micronaut; Harden Micronaut route authorization rules. Part of cursor-rules-java project

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Use when you need to design, review, or improve REST APIs with Quarkus REST (Jakarta REST) — including resource classes, HTTP methods, status codes, request/response DTOs, Bean Validation, exception mappers, optional runtime OpenAPI exposure (SmallRye), contract-first generation from OpenAPI, content negotiation, pagination, sorting and filtering, API versioning, idempotency (Idempotency-Key), optimistic concurrency (ETag / If-Match), HTTP caching (Cache-Control), API deprecation (Sunset / Deprecation headers), RFC 7807 Problem Details, ISO-8601 for time in contracts, and security-aware boundaries. This should trigger for requests such as Review or improve JAX-RS resources in a Quarkus project; Design HTTP APIs with validation and error handling on Quarkus; Add API versioning, idempotency, ETag concurrency, or deprecation headers; Implement pagination, sorting, or RFC 7807 Problem Details error responses. Part of cursor-rules-java project

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PHP Standards Recommendations (PSR) overview knowledge base. Provides comprehensive reference for all accepted PSRs including PSR-1,3,4,6,7,11,12,13,14,15,16,17,18,20. Use for PSR selection decisions and compliance audits.

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Use when you need to design, review, or improve security in Spring Boot applications — including SecurityFilterChain, OAuth2/JWT resource server patterns, form login basics, method security (@PreAuthorize), CSRF and CORS for APIs, session fixation, security headers, exception handling, password encoding, and sensitive-data-safe logging. This should trigger for requests such as Add Spring Boot security support; Review Spring Boot security configuration; Improve API authorization in Spring Boot; Add JWT resource server security in Spring Boot; Harden Spring Boot security headers and CSRF settings. Part of cursor-rules-java project

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Use when you need to apply Java secure coding best practices — including validating untrusted inputs, defending against injection attacks with parameterized queries, minimizing attack surface via least privilege, applying strong cryptographic algorithms, handling exceptions securely without exposing sensitive data, managing secrets at runtime, avoiding unsafe deserialization, and encoding output to prevent XSS. This should trigger for requests such as Review Java code for secure coding. Part of cursor-rules-java project

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Guides the creation of agile user stories and Gherkin feature files. Use when the user wants to create a user story, write acceptance criteria, define Gherkin scenarios, or author BDD feature files. This should trigger for requests such as Create a user story; Write a user story; I need to write a user story. Part of cursor-rules-java project

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Generates audit trail infrastructure for entities. Implements IAuditable interface, EF Core SaveChanges interceptor, and automatic population of CreatedAt, UpdatedAt, CreatedBy, and UpdatedBy fields.

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Put two or more Japanese job offers on one basis so they can be read side by side, separating fixed overtime allowance and unguaranteed bonus from the stated annual figure, converting each offer to guaranteed annual pay and to an hourly rate that includes deemed overtime hours, and listing non-monetary terms without scoring them. Use when a user holds more than one offer, wants to know what a stated 年収 actually contains, or wants to see where the ranking changes once the components are separated; do not use to recommend which offer to accept, to score or rank offers, to estimate take-home pay as fact, or to reply to an employer.

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Plan a resignation and the move to a new employer: check the intended notice date, last working day, and start date against the notice period the employer's own rules require, count the weekdays left against remaining paid leave, and work through the checklist of handover, documents to receive, items to return, and the insurance, pension, and residual tax steps that a gap between jobs creates. Use when a user has accepted an offer and needs to work out when and how to resign, or wants to know what to confirm before giving notice; do not use to rule on whether they can legally leave, to judge a non-compete clause, to promise the departure will go smoothly, or to notify anyone.

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Prepare the internal case for hosting an Otameshi Tenshoku trial: total what it costs the company with candidate pay, staff hours and platform or incidental fees kept apart, compare it with the budget, state what remains if no hire follows, and lay out the risks, stop conditions, decision owners and deadlines. Use when a hiring manager needs approval or budget from a decision maker, a recruiter has to explain the plan to the team that will host, or a small-business owner wants to see the full cost including their own time before posting; do not use to design the work (trial-work-design), to write the listing (trial-listing-draft), to predict whether a hire will follow, to state platform fees, agency fees or market rates from memory, or to submit the request or post the listing on the user's behalf.

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Check the terms of a specific side-work assignment offered as gyomu-itaku or freelance work in Japan, item by item: what the client has actually put in writing about the deliverable, the fee, the payment due date, what counts as out of scope, how many revisions are included, who bears expenses, who owns the result, confidentiality, and how either side can end it. Convert the fee into an effective hourly figure over the hours the work will really take including meetings, revisions and unpaid preparation, and count the days from delivery to the payment due date. Use when someone is offered or is discussing a paid side job, a freelance assignment, spot consulting, or paid trial work and wants to know what is still unwritten before starting; do not use to judge whether the fee is fair or the terms lawful, to decide whether to accept, to draft or sign the contract for the user, or to check whether their employer's rules permit side work, which is sidework-rules-check.

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Triage a GitHub issue that already has the cc-issue-created label and is assumed ready to start. Inspect the comment history first to decide whether human confirmation is needed (cc-need-human-check, highest priority — reserved for issue-level deadlock, or for confirmation items answer-issue-questions already investigated and explicitly marked unanswerable); otherwise close the issue as not needed, delegate unanswered confirmation items in the last comment or the description to answer-issue-questions (cc-answer-issue-questions), refresh a description stale relative to settled comment-history content (cc-update-issue), or move to execution (cc-exec-issue). Any UI-changing issue is routed to the design-first flow (cc-create-ui-design) before execution; the exceptions are an issue whose description already names the .pen design to implement against, and a minor UI change that introduces no new visual decision (no new screen/section, no layout change, no new reusable component, no visual expression outside existing design tokens/components). Design files are never edited in the implementation PR. Dependency checks are out of scope.

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Philosophy-first writing partner for Medium with tactical depth. Combines human storytelling values with production-ready technical content tools. Six content modes based on staff pick analysis, mode-specific quality gates, evidence requirements, annotated examples, and comprehensive scripts integration. Designed for sustainable practice, not algorithm gaming.

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Read the network instead of the DOM. Snoop JSON API responses, wait for a request instead of sleeping, collect items while scrolling, record a QA flight trace (jsonl, HAR, screenshots), and intercept requests with routes.

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Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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Compares Hi-C contact maps between conditions across the right scale -- differential bin-pair contacts (multiHiCcompare, diffHic), differential A/B compartments (dcHiC), differential TAD boundaries (delta insulation), and differential loops (diffloop, DiffHiChIP) -- with distance-stratified between-sample normalization, replicate-aware NB-GLM FDR, HiCRep SCC reproducibility gating, and CNV correction for cancer/aneuploid samples. Use when comparing Hi-C between treatment and control, finding differential contacts/compartments/boundaries/loops, normalizing two maps of unequal depth, choosing a replicate-aware test, gating replicates with SCC, or correcting copy-number artifacts before a tumor-vs-normal comparison.

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Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across samples until normalized, the CPM/RPKM/BPM/RPGC normalization menu and the conserved-total assumption that makes them wrong under a global perturbation, the strict sorted-non-overlapping-chrom.sizes bedGraphToBigWig contract that silently corrupts a bigWig, effective-genome-size selection, and bin-size aliasing. Use when building or normalizing a coverage/signal track from a BAM, comparing tracks across samples or conditions, converting bedGraph to a browser-ready bigWig, or diagnosing a track that looks plausible but reports wrong heights.

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Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates). Covers paired vs unpaired vs interaction designs, batch confounding (antibody lot, RNA prep, sequencing run) and the per-lot meta-analysis strategy when exomePeak2 is the primary caller, the stoichiometry-vs-expression-vs-IP-efficiency confound that all MeRIP differential methods inherit, normalisation choice (size factor on IP, on input, on per-sample IP/input ratio), the McIntyre 2020 reproducibility caveat, effect-size filtering as a guardrail against under-powered N=2 designs, and orthogonal-validation routes for absolute stoichiometry (GLORI / SAC-seq / m6Anet `mod_ratio`). Use when comparing m6A levels across two or more conditions, choosing between exomePeak2 / QNB / RADAR / MeTDiff for a given design, handling batch confounding when exomePeak2's API is too rigid, normalising against input properly, distinguishing real hyper- / hypo-methylation from expression-level shifts, applying effect-size thresholds, interpreting volcano plots of differential peaks, or planning a follow-up orthogonal stoichiometry validation.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.

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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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