「order」の検索結果

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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Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

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Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-stabilizing transforms (logicle/biexponential, arcsinh, log) for flow and mass cytometry. Covers spillover-matrix estimation from single-stain controls, AutoSpill, the spillover spreading matrix and why panel design (not compensation) bounds resolution, compensate-then-transform ordering, and arcsinh cofactor choice (5 for CyTOF, ~150 for fluorescence, per-channel via flowVS). Use when correcting spectral overlap, preparing data for gating/clustering, choosing logicle vs arcsinh, deciding a cofactor, or distinguishing compensation from spectral unmixing.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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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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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DTL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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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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Use when working in a multi-module Maven project. Covers parent POM conventions, shared dependency management, inter-module rules, and build ordering.

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Retro arcade-inspired design with pixel fonts, dotted borders, playful high-contrast colors, and 8-bit game aesthetics.

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Dynamic, vibrant style with thick borders, geometric shapes, high-contrast colors, and expressive typography conveying motion and vitality.

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Frosted glass effect with translucent layers, subtle blur, and luminous borders for depth and modern elegance.

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Playful, minimal design with bright colors, rounded shapes, tactile 3D borders, and friendly illustrations for approachable interfaces.

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Modern take on brutalism with bold borders, vivid accent colors, and raw, high-contrast layouts on warm surfaces.

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Canonical design token registry — colors, typography, spacing, sizing, border radius, shadows, z-index, breakpoints, motion, and focus tokens. Used by ui-best-practices rules and all agents that implement or review UI components. Includes CSS variable template for quick project setup.

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Use when the user wants a backend-only action plan — API endpoints, services, models, migrations, jobs and their tests — 'plano de backend para o endpoint X', 'plan the orders API'. Writes .planning/feat/features/{slug}/plan.md with the PWDEVIA method. Do NOT use for UI work (feat-frontend), full features spanning backend and UI (feat-feature), writing code (feat-exec) or quick 1–3 file fixes (feat-quick).

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Sequential multi-step setup flow (assistant/wizard) with AdwNavigationView, Back/Forward navigation, progress indication. Use when building onboarding or setup flows with ordered steps.

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Auto-review pipeline — reads the full CEO, design, eng, and DX review skills from disk and runs them sequentially with auto-decisions using 6 decision principles. Surfaces taste decisions (close approaches, borderline scope, codex disagreements) at a final approval gate. One command, fully reviewed plan out. Use when asked to "auto review", "autoplan", "run all reviews", "review this plan automatically", or "make the decisions for me". Proactively suggest when the user has a plan file and wants to run the full review gauntlet without answering 15-30 intermediate questions. (gstack) Voice triggers (speech-to-text aliases): "auto plan", "automatic review".

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Refactor and review SwiftUI view files for consistent structure, dependency injection, and Observation usage. Use when asked to clean up a SwiftUI view’s layout/ordering, handle view models safely (non-optional when possible), or standardize how dependencies and @Observable state are initialized and passed.

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Generate realistic, correctly-linked Frappe/ERPNext test records for any DocType using the `bench faker` CLI, then roll them back when done. Use when a test, demo, or local repro needs seed data and the site is missing it — e.g. "I need some Sales Orders", "seed data so I can test this API", "create test Employees in Chennai", or "populate the database to test this endpoint".

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Validate process decomposition and architecture design quality before execution begins. Load when the setup-evaluator agent fires (automatic for agent-chain tasks), or when user says "evaluate this setup", "check the decomposition", "validate the architecture", "is this plan sound", "review the agent design". Catches structural errors, missing knowledge, unrealistic step ordering, and topology mismatches. Does NOT modify — only evaluates.

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Decompose an unknown quantity into 3-5 estimable factors and produce a defensible order-of-magnitude answer without needing precise data. Load when the user needs to size something without data — market size, resource requirements, effort estimates, user numbers, costs — or when a decision is blocked by "we don't know the numbers". Also triggers on "ballpark this", "rough estimate", "how big is this market", "how long would this take", "how many users", or when deep-thinking diagnoses a sizing/estimation frame. The goal is not precision — it is a defensible answer that enables a decision to be made. Based on Enrico Fermi's estimation method.

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