「conditions」の検索結果

Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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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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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers between conditions, identifying master transcription factor networks, or predicting BET-inhibitor responsiveness.

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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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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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Use this skill to understand FMCSA cardiac certification standards. Covers what cardiac conditions disqualify, time-to-clearance, and what documentation is needed for examiner certification.

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Use this skill when the user asks specifically about preparing for the New Entrant Safety Audit (NESA) under 49 CFR 385 Subpart D — different from a Compliance Review. Covers what auditors look at, the 18-month window, automatic failure conditions, the 60-day fix window, what to NOT do, and how to convert from "new entrant" to permanent authority. Cite 49 CFR 385.301-321.

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Use this skill when the user asks about Hours of Service (HOS) rules under 49 CFR 395 — the 11-hour driving limit, 14-hour on-duty window, 60/70 hour rule, 30-minute break, 10-hour off-duty reset, 34-hour restart, sleeper berth provisions, split sleeper berth, short-haul exemption (150-air-mile), agricultural exemption, adverse driving conditions, ELD malfunction handling, personal conveyance, yard moves, or anything related to driver duty status. Cite specific 49 CFR 395 subsection. If the question involves a non-standard operation (passenger carrier, oilfield, agricultural, military), confirm which set of rules applies.

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Use this skill when the user asks about CDL driver medical certification — 49 CFR 391.41-49 medical qualifications, medical examiner's certificate (Long Form 5876 + Short Form 5875), National Registry of Certified Medical Examiners (NRCME), medical restrictions, federal disqualifying conditions, exemption programs (vision, diabetes, hearing), the FMCSA Medical Examiner's Handbook, or what to do when a driver's medical cert is downgraded. Cite specific 49 CFR 391 sections.

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Use this skill when the user asks how to interpret a DOT medical examiner's findings — what restrictions mean (corrective lenses, hearing aid, no insulin, etc.), what conditions trigger short-term vs 24-month certificates, vision/hearing thresholds, blood pressure categories, sleep apnea screening, when to seek an exemption program, and how to handle a downgrade or denial. Cite 49 CFR 391.41-49 and the FMCSA Medical Examiner Handbook.

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Use this skill when hiring a driver who has a recent valid pre-employment test from a prior employer. Covers the conditions under § 382.301(c) that allow accepting it instead of testing again.

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Use this skill when the user asks about Americans with Disabilities Act (ADA) accommodation for CDL drivers — interaction between ADA + FMCSA medical certification, when DOT-disqualifying conditions trigger ADA analysis, reasonable accommodation case examples, employer obligations, and how to handle a driver with a condition that may affect CDL status. Cite Title I ADA + 49 CFR 391.41.

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Define initial conditions and predefined fields. Use when user mentions initial temperature, pre-stress, residual stress, or import from previous analysis.

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Define boundary conditions - fixed supports, displacements, symmetry. Use when user mentions fixed, pinned, clamped, supported, or constrained. Does NOT handle loads or forces.

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Library of accessibility personas representing people with various disabilities, impairments, and situational limitations. Use this skill when users ask about disability types, accessibility personas, user needs for specific conditions, how people with disabilities use technology, assistive technology users, or designing for accessibility. Triggers on requests about blindness, deafness, cognitive disabilities, motor impairments, low vision, screen readers, sign language, autism, ADHD, temporary disabilities, or any question about "how would a person with X use this".

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Analyze market conditions, geographic opportunities, pricing, consumer behavior, and product validation across Google Maps, Facebook, Instagram, Booking.com, and TripAdvisor.

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Use this skill when building analytics dashboards with nuxt-ui-tools as a package consumer. Covers schema and view functions (defineDashboardSchema, defineDashboardView) that take their context as typed params, useDashboard with a getter that rebuilds on input change, typed injection (useDashboardView, injectDashboard, InferDashboard, InferDashboardView), filters declared inline with the f builder and synced with the URL, memory, or an external store (one value per key across views), headless filters, filter controls and the shipped UI (UiDashboardPage, UiDashboardFilters, UiDashboardFilter, UiDashboardViewTabs) with slot overrides, remote paginated pickers and remoteTableOptions, staged queries (essential / background / deferred) with select and dependent requires, lazy enabled conditions on views, queries, and filters (blocks of disabled queries hidden, grids closing up), derived values, views (tabs), query-scoped filters, number formats (presets, Intl options, useDashboardFormat), and the dashboard blocks (stats with trends, goals, and comparisons, stat groups, gauges, unovis charts with highlights, value labels, and totals, lists with progress rings, bars, funnel, alerts, activity feeds, sortable tables, custom widgets) with their automatic loading, error, empty, and refresh states, card menus, header and footer actions, row actions, drill-down and selected state, card tabs, split cards, comparison periods, auto-refresh, and data freshness.

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