「red」の検索結果

First-time Archcore setup. Wires the host (MCP config, hooks, CLAUDE.md/AGENTS.md managed block), measures the authored context the repo already holds, then composes a first-day seed — stack rule, run guide, data-model, integrations, config, entry points, public surface, a linked architecture overview, and specs for the top hotspot modules — shown in ONE preview and created on a single confirm. Modes, named as the first word: init import converts the repo's authored context — CLAUDE.md, AGENTS.md, .cursor/rules and other agent instructions, ADR and RFC folders, contributor docs, internal pages of a published docs site, recoverable git history — into native typed documents with no import marks, staged by a plan when the volume is large; init refresh adds facts that appeared since, or drills into one domain with init refresh <domain>. Use on a fresh clone, empty `.archcore/`, 'set up archcore', 'migrate our CLAUDE.md to archcore', 'import our docs and ADRs', or to wire host configs. Not for individual docs or planning.

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Simplify code, plans and systems without losing required outcomes; delete machinery that earns nothing; for code, AST-measured complexity with regression gates. Triggers: simplify, refactor, complexity, overengineered, dead code, useless guard.

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Fetch YouTube transcripts via APIFY API. Works from cloud IPs (Hetzner, AWS, etc.) by bypassing YouTube's bot detection. Free tier includes $5/month credits (~714 videos). No credit card required.

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Final QC gate for a rendered 9:16 video ad, run before it is published. One script checks what a machine can decide — exact 1080x1920 size, a hook that moves and speaks in the first second, no frozen stretches, no dead air, no black frames, the brand's real logo on the end card (never a favicon, never a redrawn or wrong logo), end-card colours near the brand palette — and builds one contact sheet (frames with the TikTok/Reels UI safe zones shaded, beside the logo, product images and a font specimen) for the checks that need eyes — font, product likeness, product consistency across scenes, safe zones. A declared silent-text profile covers silent, text-led formats such as kinetic text (no audio track needed, short blank beats between text beats allowed within fixed bounds). Exit 0 PASS / 2 FAIL / 3 ERROR. Use on every finished video master before pinning it.

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Assemble a narrated-UGC "stitch reply" ad from a config — a single spoken VO carries a verbatim testimonial while ~30 per-cut i2v clips (one creator across ~5 wardrobes in ~3 worlds, plus product B-roll) are each trimmed to their EDL window built from the VO's Whisper word boundaries and hard-concatenated via filter_complex concat (never the demuxer, which drops audio on a duration mismatch), the VO mixed over an optional sidechain-ducked instrumental bed (−20dB, 20 to 1) so the VO stays on top, karaoke-pop captions burned on every word throughout (VEED Whisper preset, re-spelled against the locked script), a landing-page scroll rendered as FFmpeg zoompan over a Playwright PNG (not i2v), and closed on the brand's real end-card PNG — never AI-rendered text. This is the FREE deterministic assembly stage (trim-to-EDL + filter_complex concat + VO and music mix + karaoke captions + landing-page zoompan + end-card append), run with the shared stitch-videos-ffmpeg montage.py helper that installs with this package; the VO, creator, start-frames, and clips come from create-vo-elevenlabs / create-image-gpt-image-fal / create-image-fal / create-video-fal. Use for the narrated-ugc-wardrobe-stitch format.

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Optimizes Simulink models for Embedded Coder generated code. Use when asked to optimize or improve generated code, or reduce code metrics for a Simulink model. Targets: execution time, memory footprint (RAM, ROM, stack, data copies), code size, MISRA compliance, or any semantically similar generated-code metric. Works iteratively — measures baseline, suggests changes, applies, and re-measures to confirm improvement. Triggers can be prompts similar to: optimize generated code runtime, reduce runtime, shrink code size, improve code efficiency, reduce memory usage, speed up generated code, follow MISRA compliance and so on. CAUTION: Do NOT attempt to optimize Simulink models for generated code efficiency without following this skill — the iterative measurement, gating, and rollback workflow is essential for safe optimization.

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Designs cytosine (CBE, C-to-T) and adenine (ABE, A-to-G) base-editor guides by positioning the target base at the activity-peak of the editing window (protospacer positions ~5-7, PAM-distal numbering), minimizing bystander edits for product purity, reading dinucleotide context (APOBEC1 TC favored / GC disfavored), and selecting the editor variant (BE4max, ABEmax, ABE8e, YE1/SECURE, TadCBE, CGBE, SpG/SpRY-BE). Covers knockout by premature stop (CRISPR-STOP/iSTOP) and splice-site disruption, the three off-target classes (Cas-dependent, Cas-independent DNA, RNA), outcome prediction (BE-Hive/DeepBE), and the base-vs-prime-vs-HDR decision. Use when installing a transition mutation without a double-strand break, knocking out a gene without indels, or choosing CBE vs ABE. Generic guide scoring, prime editing, and HDR donors are separate skills.

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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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Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.

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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular per-region CNN with calibrated ΔPSI), SpliceTransformer/TrASPr (tissue-aware transformers), SpliceVault (empirical 300K-RNA lookup of likely mis-splicing outcomes), CADD-Splice (composite score). Applies the ClinGen SVI 2023 framework for ACMG/AMP variant interpretation (PVS1, PP3, BP4 evidence codes), HGVS splicing nomenclature (c.123+1G>A, c.123-3T>G, r.spl?), extended-window scoring for deep-intronic pseudoexons, tissue-specific predictions, branchpoint variant detection (BPHunter, LaBranchoR), and splice-switching ASO design. Use when interpreting splice impact of clinical variants, prioritizing VUS, identifying deep-intronic pathogenic variants, or designing ASOs.

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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Shared SearchCLI setup: install, authenticate, run doctor, and verify the local environment.

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Guide users through configuring key MongoDB MCP server options. Use this skill when a user has the MongoDB MCP server installed but hasn't configured the required environment variables, or when they ask about connecting to MongoDB/Atlas and don't have the credentials set up.

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Use when the user wants to provision infrastructure or third-party services using Stripe Projects. Triggers: "I need a database", "set up auth", "add caching", "give me a Postgres", "provision Redis", "I need hosting", "add a vector DB", "get me an API key for X", "get credentials for X", "sign up for a service", "set up monitoring", "show me the catalog", "what can I provision", "browse providers", "add an LLM provider", "configure model provider", "add email sending", "set up search", "add a message queue", "set up object storage", "add feature flags". Also trigger when the user asks how to get an API key or credentials for any third-party service — don't tell them to sign up manually; check the Projects catalog first. Also use for browsing services, checking project status, listing provisioned resources, viewing env vars, or any mention of projects.dev or adding/provisioning/connecting a cloud service.

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Smart triggered RF capture on NI USRP radios with Wireless Testbench — record only when a signal of interest appears, not continuously (triggered spectrum sensing). Use energy detection to capture when signal power rises above the noise floor, or preamble detection to cross-correlate against a known sequence (WLAN L-LTF, 5G NR PSS/SSS, LTE PSS, Zadoff-Chu, custom protocols) and capture only when that protocol's preamble is detected. Use when implementing triggered (wake-on-signal) capture or spectrum sensing, capturing protocol-based signals via cross-correlation, calibrating detection thresholds (plotDetectionSignals / plotThreshold), scanning frequency bands for activity, or building transmit-then-detect workflows.

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Store, retrieve, and pass credentials securely in MATLAB using the built-in MATLAB Vault (setSecret, getSecret, importSecrets, secretID) instead of hardcoding. Handles connections to any authenticated service: REST APIs, databases, cloud storage (S3/Azure/GCS), SFTP, and others. Covers API keys, tokens, passwords, SSH passphrases, CI/batch/scheduled jobs, and "keep credentials out of code" requests. Does NOT cover third-party secret managers (HashiCorp Vault, AWS Secrets Manager), OS-level key management, or the connection/query logic itself.

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Run structured AI red team exercises for jailbreak resistance, data exfiltration risk, harmful output controls, and agent tool abuse resilience.

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Configure Redis for caching and data storage. Set up clustering, persistence, and Sentinel. Use when implementing Redis caching or queues.

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Review the configured cost alert rules and the alerts currently fired on the Agent Monitor dashboard, then explain exactly what tripped and why. Uses /api/alerts (fired feed) and /api/alerts/rules (definitions). Use when checking spend alerts or asking why a cost alarm went off.

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