「screening」の検索結果

Generates complete FAERS-style pharmacovigilance disproportionality research designs from a user-provided drug class, comparator strategy, adverse-event domain, and patient-group stratification. Always use this skill whenever a user wants to design, plan, or build a spontaneous-report safety signal study using FAERS or a similar pharmacovigilance database, especially when the article logic includes product selection, indication-group stratification, MedDRA-based adverse-event extraction, serious-case filtering, suspect-drug and concomitant-exclusion logic, reporting odds ratio analysis, comparator-drug benchmarking, cross-drug comparison, and cautious signal interpretation without causal overclaiming. Covers five study patterns (single-drug disproportionality workflow, multi-drug class comparison workflow, indication-stratified workflow, comparator-controlled signal screening workflow...

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Generates complete NHANES-style cross-sectional epidemiology + retrospective clinical validation research designs from a user-provided disease and biomarker direction. Always use this skill whenever a user wants to design, plan, or build a population-level biomarker association study using NHANES or similar survey datasets, especially when the article logic includes disease definition, biomarker formula derivation, multivariable logistic regression, restricted cubic spline analysis, subgroup stability testing, and a secondary hospital-based retrospective validation cohort. Covers five study patterns (cross-sectional association, dose-response / RCS, subgroup-stability, NHANES + retrospective validation, preliminary screening-performance) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path...

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Generates complete bidirectional multi-phenotype Mendelian randomization research designs from a user-provided exposure family and outcome family. Always use this skill whenever a user wants to design, plan, or build a genome-wide causal-inference study based on publicly available GWAS summary statistics, especially when the article logic includes multiple exposures, multiple outcomes or subtypes, bidirectional MR, IV filtering, IVW as the main estimator, weighted median / MR-Egger / MR-PRESSO sensitivity analyses, leave-one-out testing, heterogeneity / pleiotropy checks, and multiple-testing control with FDR. Covers five study patterns (single-family bidirectional MR, multi-phenotype screening MR, subtype-resolved MR, phenome-style bidirectional causal map, mechanism-prioritized MR follow-up) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version...

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Use when assessing how well a survival model's predicted probabilities agree with observed outcomes by fitting a Cox model and generating bootstrap calibration curves at one or more prediction horizons from a clinical CSV file. NOT for: nomogram construction, univariate Cox screening, ROC analysis, or decision-curve analysis.

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Use when constructing a prognosis nomogram from survival-related clinical predictors, exporting the nomogram bundle and C-index table, and optionally rendering the final nomogram PDF. NOT for: univariate/multivariable Cox feature screening, calibration curves, ROC analysis, decision-curve analysis, or non-survival outcomes.

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Use when running prognostic survival analysis on a clinical cohort with time-to-event data to estimate univariate and multivariable Cox proportional hazards models, export result tables, and generate forest plots. NOT for: nomogram construction, calibration curves, time-dependent ROC analysis, or model training/feature selection beyond the built-in univariate screening rule.

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Quickly judges whether a biomedical paper is worth deep reading by screening for question fit, design quality, sample adequacy, methodological novelty, and reproducibility value.

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Generate the submission-time disclosure block for a manuscript — the AI-use disclosure statement matched to the target journal's policy, CRediT author-contribution roles, conflict-of-interest statement, and data-availability statement. Use when the user says "AI disclosure", "disclosure statement", "do I need to disclose Claude", "CRediT roles", "conflict of interest statement", "data availability statement", or is preparing a submission package. NOT statistical-disclosure screening of restricted-data outputs — that is /disclosure-check.

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Check whether a raise, more hours, or a new job could cost you more in lost benefits than you gain — the 'benefits cliff' — before you accept it. Use when asked will a raise hurt my benefits, benefits cliff, if I make more will I lose my food stamps or medicaid, or should I take more hours. Produces a plain map of which benefits phase out at what income (and which cut off suddenly vs. taper), a rough read on whether a specific income change helps or hurts net, the ones with hard cliffs to watch (childcare, Medicaid, housing), the moves that soften a cliff, and where to get a real benefits screening. Not financial/benefits advice; points to a benefits counselor.

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Use when you need to understand how American Anthropologist (AA) evaluates a manuscript — editorial screening, anonymous peer review under an ethics of care, the four-field editorial board, decision categories, and how section choice shapes the path. Sets expectations and shapes the paper to survive review; it does not contact editors.

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Use to understand how Agricultural Systems (AgSy) evaluates a manuscript — single-anonymized peer review with a minimum of two reviewers and an editor decision, desk screening for fit and systems content, what reviewers weigh, and the rapid-review track for Perspectives. Sets expectations and shapes the paper to survive review; it does not contact editors.

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Identity verification via phone/email OTP and AML screening using Didit API

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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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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Detects m6A modifications from Oxford Nanopore direct-RNA-seq (DRS) signal using m6Anet (multiple-instance-learning over DRACH 5-mer signal). Covers the upstream pipeline (Dorado/Guppy basecalling -> minimap2 map-ont -> nanopolish eventalign -> m6anet dataprep -> m6anet inference), per-site vs per-read probability including the mod_ratio stoichiometry column, the DRACH-only constraint, minimum-coverage thresholds (20-50 reads/site), multi-condition comparison via xPore/Nanocompore/ELIGOS, Dorado native modification calling (RNA004, 2024+), and the cDNA-vs-DRS distinction (cDNA Nanopore CANNOT detect modifications). Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting probability_modified vs mod_ratio vs per-read probabilities, deciding between m6Anet (known DRACH sites) and Dorado/Remora (genome-wide screening), pinning RNA002 vs RNA004 chemistry and basecaller versions, or troubleshooting eventalign/dataprep failures.

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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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Performs retrosynthetic planning using AiZynthFinder (template-based MCTS), maintained or version-pinned template-free models, ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, configurable MCTS rewards, building-block availability, and forward-prediction checks. Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, HLA-LA, T1K, Polysolver, HLA-HD, arcasHLA, StarPhase, or HIBAG imputation. Use when typing for HSCT, solid-organ transplant, neoantigen prediction, PGx screening (B*57:01, B*15:02, etc.), or disease-association studies, with reconciliation across tools and IPD-IMGT/HLA version mismatch handling.

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。