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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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Technical SEO audit across 8 categories: crawlability, indexability, security, URL structure, mobile, Core Web Vitals, structured data, JS rendering. Schema deep validation → seo-schema. AI crawlers → seo-geo-technical. Use when user says "technical SEO", "crawl issues", "robots.txt", "Core Web Vitals".

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ゴール駆動オーケストレーション - rubric ファーストの自己修正 BUILDING ループ

Plan the first months at a new Japanese employer after an offer is accepted, listing every expectation and promise made in interviews, the offer, or negotiation with its source, separating what is in writing from what was only said and what has no agreed measure, working out when the probation period ends and whether its criteria and conditions are known, and scheduling who to confirm what with before and after the start date. Use when a user has accepted an offer and wants to prepare for joining, make sure verbal promises such as remote days or a future role are confirmed, or understand what the probation period means for them; do not use to predict whether they will fit in or pass probation, to judge their manager or colleagues, to rule on the legality of probation terms, or to contact the new employer.

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Help job seekers use Otameshi Tenshoku to prepare profiles and applications, clarify trial conditions, plan learning visits or paid trial work, and reflect on the experience. Use when a candidate wants to apply for, prepare for, negotiate the scope of, or review an otameshi work experience; do not use to predict whether they will be hired or to judge their aptitude, to state fees, contract terms, or service conditions from memory, or to submit an application, update a profile, or send a message on their behalf. Employer-side requests belong to the employer skills (trial-work-design, trial-listing-draft, applicant-reply and others).

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Lay out how a job search will actually run alongside a current job: the hours available each week and what they go to, how weekday daytime slots for interviews will be found, which routes to use (direct applications, job boards, scout sites, agents, referrals, public employment services) and what each one discloses to whom, how to keep the search from reaching the current employer through public profiles or workplace equipment, a single tracker of every application's stage, next action, and deadline, and a date and conditions for reviewing, reducing, or pausing the search. Use when someone has decided to start looking, or to gather information while employed, and asks how to fit it in, which routes to use, whether the applications they are running fit the time they have, or how to keep track of them; do not use to decide whether to change jobs, to pick or rate employers or job postings, to predict outcomes, or to send applications, publish profiles, or contact agents on the user's behalf.

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Go through an interview that has just finished and sort out what happened: the questions asked and how fully they were answered, which of them were prepared for and which came from the submitted documents, the reverse questions still unanswered, what the employer said about conditions and whether any of it was in writing, and when a result was promised. Use when a user has just come out of an interview and wants to record it while it is fresh or to work out what to fix before the next round; do not use to judge how it went, to estimate whether they will pass, or to read anything into the interviewer's manner.

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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 a request to change the terms of a Japanese job offer before accepting it, sorting what the user wants changed (pay components, start date, work style, location, title, probation) by priority, tying each ask to a basis the user can show (the written offer, the job posting, what was said in interviews, their own records), working the timing back from the acceptance deadline, and drafting the message to the employer or recruiting agent. Use when a user has an offer and wants to ask for higher pay, a later start date, more remote days, or other changed terms, or wants to know how to raise it without losing the offer; do not use to predict whether the request will succeed, to set a target figure from market rates, to fabricate a competing offer, to decide whether to accept, or to send anything to the employer.

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Shakes your mental models with critical rigor, challenges assumptions, exposes blind spots, and provides multi-perspective insights as a strict thinking mentor. Deliberately breaks format conventions to stimulate genuine cognitive discomfort. Use when you want to stress-test an idea, shake your mental model, ask to challenge my assumptions, find blind spots, deepen my thinking, or request critical review with phrases like yusaburi or what do you think of this plan.

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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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DON'T USE THAT SKILL. IT'S JUST AN EXAMPLE. Summarize today's Gmail inbox by category with anonymized senders and subjects, then surface the top 3 emails to focus on next. Run only when the user types /email-summary.

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Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Renders Hi-C contact matrices honestly and reproducibly with matplotlib, cooltools, HiCExplorer, pyGenomeTracks, FAN-C, CoolBox, and plotgardener. Covers the raw/ICE-balanced/observed-over-expected transform choice, LogNorm vs symmetric-diverging colormaps with vmax/percentile clipping, resolution-to-feature matching (compartments 100-500kb, TADs 10-40kb, loops 5-10kb), square vs rotated-triangle track-stacking, NaN/white-stripe handling, virtual 4C, APA/saddle/on-diagonal pileups, two-condition side-by-side and log2-ratio maps, and interactive (HiGlass) vs scripted-static publication figures. Use when plotting a contact matrix, choosing a normalization or color scale, building a multi-track Hi-C figure, making a virtual 4C profile, piling up loops/boundaries, or comparing two conditions.

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Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation) and HiCExplorer hicFindTADs, returning a continuous log2 insulation track, valley-prominence boundary_strength, and Li/Otsu-thresholded is_boundary flags across a list of window sizes. Covers the multi-scale window sweep (sub-TAD to compartment-domain), why the boundary is reproducible but the domain partition is not, cross-condition comparison via differential SCORE not differential partition, and the insulation-vs-compartment orthogonality. Use when calling TADs or domain boundaries, computing insulation scores, choosing a window size, ranking boundary strength, comparing boundaries across conditions, or annotating CTCF-backed boundaries; route domain rendering to hic-visualization and boundary-feature overlap to genome-intervals.

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Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expected_cis per-diagonal P(s), expected_trans scalar), builds observed/expected (O/E) matrices, and diagnoses polymer state from the P(s) log-derivative. Covers the within-matrix-vs-cross-sample distinction (balancing is NOT a normalizer), the equal-visibility assumption that CNV/aneuploidy violates (use raw counts for copy-number), cis-only balancing, mad_max/blacklist masking before balancing, multiplicative cooler weights vs divisive juicer weights, and the resolution-vs-depth budget. Use when balancing a .cool/.mcool, computing expected or P(s), making O/E matrices for compartments/loops, deciding ICE vs KR vs SCALE, choosing a resolution for a given depth, or troubleshooting NaN/all-NaN balanced matrices; route cross-sample comparison to hic-differential.

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Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.

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Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.

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Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE for visualization. Covers the type-vs-state marker distinction (cluster on lineage, test state within clusters), over-provision-then-metacluster, the Weber-Robinson benchmark, seed dependence and metacluster stability, why embeddings are for looking not measuring, and median-heatmap annotation/merging. Use when discovering populations without predefined gates, choosing a clustering algorithm, selecting the number of metaclusters, or annotating clusters into cell types.

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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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Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.

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Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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。