2,059 件 ・ 関連度順
概要と使いどころ
API gateway and reverse proxy configuration with Kong, Nginx, Traefik, routing, and auth middleware. Activate on: API gateway, reverse proxy, Kong, Nginx, Traefik, load balancer, ingress, auth middleware. NOT for: rate limiting algorithms (use api-rate-limiting-throttling-expert), service mesh (use service-mesh-microservices-expert).
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How to design contextual inputs for an always-on AI agent with episodic memory. Covers what data to feed the agent, how to structure observations and triggers, ambient context capture (screen, audio, calendar), context window budgeting, and retrieval strategies that keep the agent grounded in what's actually happening. Activate on: "what should the agent observe", "context inputs for agent", "ambient context capture", "agent triggers", "agent input design", "screenpipe integration", "context window budget", "what data to feed my agent", "/always-on-agent-inputs". NOT for: memory architecture and storage (use always-on-agent-architecture), application ideas (use always-on-agent-applications), safety concerns (use always-on-agent-safety).
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Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.
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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.
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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.
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Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding. Covers pegRNA design with PRIDICT and PRIDICT2 for predicting per-pegRNA editing efficiency, pegRNA architecture (spacer + scaffold + PBS + RTT), PE2/PE3/PE3b/PEmax variants, MOSAIC in situ saturation mutagenesis, the PRIME pooled-screen methodology (Ren 2023; ~3,699 ClinVar variant screens), chromatin context as a major locus-level determinant of PE efficiency, scaffold-incorporation and indel byproduct quantification with CRISPResso2, and the cross-modal validation strategy of PE + base-editor screens for variant function. Use when designing a pegRNA library for variant installation, choosing between BE and PE for a specific edit, predicting pegRNA efficiency before library synthesis, analyzing PE screen output, distinguishing intended-edit from scaffold-incorporation, or scaling PE screens to thousands of variants.
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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.
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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.
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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.
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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.
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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.
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Calculates tumor mutational burden from WES/WGS/panel data with Friends of Cancer Research harmonization equations, per-assay calibration (FDA 10/Mb = 7.8 TSO500 = 8.4 OncomineTML), synonymous/indel/germline filtering, hypermutator tiering, blood TMB, and integration with HLA-LOH and neoantigen quality (Luksza 2017 fitness). Use when assessing ICI eligibility under tumor-specific cutoffs (McGrail 2021), comparing tissue vs bTMB, or auditing TMB-H reporting against ESMO 2024 and FDA pembrolizumab pan-tumor 2020.
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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.
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Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with modeled-endpoint uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.
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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
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Agile product ownership toolkit for Senior Product Owner including INVEST-compliant user story generation, sprint planning, backlog management, and velocity tracking. Use for story writing, sprint planning, stakeholder communication, and agile ceremonies.
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This skill guides individualized prostate cancer screening for transgender females receiving estrogen therapy based on personal risk. Trigger phrase: transgender female receiving estrogens.
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This skill determines whether testicular volume should be used as the primary or sole indicator of sexual development in male childhood cancer survivors who have received gonadotoxic treatments such as alkylating agents or testicular radiotherapy. Triggers include clinician questions like “Can I use testicular volume to assess puberty in this male survivor after chemotherapy?” or “Is testis size reliable for sexual maturity evaluation post‑radiation?”
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Provides monitoring schedule for transgender females on estrogen therapy, including clinical evaluation, hormone levels, prolactin, electrolytes, BMD, and cancer screening. Triggered when a transgender female is receiving estrogen therapy for gender affirmation.
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Guidance for clinicians managing pregnant individuals with preexisting diabetes mellitus (PDM) who are evaluating daily carbohydrate intake; consider a carbohydrate-restricted diet (<175 g/day) or usual diet (>175 g/day) based on patient factors. Trigger when assessing nutrition in pregnancy for PDM, especially when discussing glycemic targets, weight gain, or fetal growth concerns.
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This skill recommends obtaining an oncology consultation to direct treatment of the underlying malignancy causing hypercalcemia of malignancy. It is triggered when a clinician diagnoses HCM and seeks guidance on coordinating cancer‑directed therapy.
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This skill recommends measuring late-night salivary or serum cortisol to screen for Cushing's disease recurrence in patients with eucortisolism after transsphenoidal surgery, including cases where eucortisolism was established by medical treatment prior to surgery. Use when postoperative follow-up shows eucortisolism (normal morning cortisol/UFC) but concern for recurrence exists.
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Recommends hydrocortisone stress dosing during the active phase of labor for pregnant patients with primary adrenal insufficiency, using a regimen similar to major surgical stress. Trigger phrases: "active phase of labor", "cervix dilation ≥4 cm", "contractions every 5 minutes", "PAI patient in labor".
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Order and interpret lipoprotein(a) [Lp(a)] measurement at least once in a lifetime, apply the risk-enhancer threshold (≥125 nmol/L or ≥50 mg/dL), and run cascade screening of first-degree relatives for premature ASCVD, familial hypercholesterolaemia, or elevated Lp(a) per the 2026 ACC/AHA multisociety dyslipidaemia guideline. Covers the Class 1 lifetime measurement, how elevated Lp(a) affects LLT initiation and intensification, the cascade screening indications, the interaction of Lp(a) with ASCVD risk estimation, and current therapeutic limitations. Use when a clinician asks when to check Lp(a), how often to repeat Lp(a), elevated Lp(a) what next, treatment for high Lp(a), should I screen my patient's family, Lp(a) and statins, cascade screening indications. Grounded in the 2026 ACC/AHA multisociety dyslipidaemia guideline.
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。