「decomposition」の検索結果

Operate as an agentic engineer using eval-first execution, decomposition, and cost-aware model routing.

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Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across conditions.

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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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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA log-fold-change as the product of a treatment-dependent gene-essentiality term and a treatment-independent guide-efficacy term. Covers the Bayesian decomposition math, the hierarchical efficacy prior shared across screens performed with the same library, when JACKS outperforms MAGeCK (multi-screen joint analysis, libraries with broad efficacy variance) and when it does not (single screen, novel libraries with no prior efficacy), library-reuse efficacy transfer, downstream essentiality interpretation, and the 2.5x sample-size reduction enabled by efficacy-aware testing. Use when running multiple screens with the same library, when guide-level noise is suspected to dominate per-gene signal, when reusing published essentiality reference screens for efficacy priors, or when comparing screens performed across cell lines that share library but differ biologically.

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Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.

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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Builds and reviews SwiftUI views with modern MV architecture, state, composition, isolated previews, and migration guidance. Covers @Observable ownership, @State/@Bindable/@Environment wiring, view decomposition, ViewModifiers, environment values, .task loading, iOS 26+ handoffs, Writing Tools, clipboard availability, and performance. Use when structuring SwiftUI state, managing @Observable, composing views, previewing meaningful UI states, or correcting SwiftUI patterns.

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Apply step-by-step analysis for complex problems with revision capability. Use for multi-step reasoning, hypothesis verification, adaptive planning, problem decomposition, course correction.

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Multi-agent orchestration for complex tasks. Use when tasks require parallel work, multiple agents, or sophisticated coordination. Triggers include requests for features, reviews, refactoring, testing, documentation, or any work that benefits from decomposition into parallel subtasks. This skill defines how to orchestrate work using cc-mirror tasks for persistent dependency tracking and TodoWrite for real-time session visibility.

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Run a structural-review debate between two lenses — lowy (volatility-based decomposition) and hickey (structural simplicity) — on the current diff. Each reviews independently, then they cross-examine every finding until they agree per-finding, and the agreed fixes are applied. Use when the user types `/lens-debate`, or asks to "have lowy and hickey review this", "run the lens debate", "debate this diff structurally", or "argue the structure of this PR until the lenses agree".

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System decomposition and dependency mapping

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CLI modernization and hooks system enhancement for claude-flow v3. Implements interactive prompts, command decomposition, enhanced hooks integration, and intelligent workflow automation.

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This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.

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Roadmap concision rules, step decomposition efficiency, AC abstraction guidelines, and step-to-scenario mapping. Load when creating implementation roadmaps.

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Coordinate nontrivial work in the ctx repository when a task has independent investigation, implementation, or test lanes; compute-heavy checks; or repetitive changes suited to scripts or codemods. Use for decomposition and concurrency decisions, not simple edits or questions.

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Knowledge base from "Solving a Million-Step LLM Task with Zero Errors" (Meyerson, Paolo, Dailey, Shahrzad, Francon, Hayes, Qiu, Hodjat, Miikkulainen — arXiv:2511.09030). Use when designing long-horizon, multi-step agentic LLM pipelines that need very high reliability, applying Maximal Agentic Decomposition (MAD), first-to-ahead-by-k voting, or red-flagging error correction, estimating cost/reliability scaling laws for multi-agent systems, or studying Massively Decomposed Agentic Processes (MDAPs).

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Investigate requirements via atomic AC decomposition, actor/permission matrices, and truth-table edge cases; enforce User Story standards (scope fences, platform tags, toggles). Use when writing/reviewing Stories or AC with multi-condition logic, feature toggles, or market variants (VN/MY/SG).

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User story generation - INVEST criteria, acceptance criteria (BDD/Given-When-Then), story mapping, epic decomposition, edge case stories, NFR stories

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Build chapter-level briefs (`outline/section_briefs.jsonl`) from chapter skeleton plus section bindings before stable H3 decomposition.

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Build a retrieval-informed chapter skeleton (`outline/chapter_skeleton.yml`) from taxonomy/core scope before stable H3 decomposition.

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Create branded architecture, architecture delta, IT current-state, flowchart, sequence, state machine, ER/data model, timeline, swimlane, quadrant, radar/spider, polar chart (polar/radial lollipop), loop/flywheel, nested, tree, org chart, layer stack, exploded axonometric, axonometric plan, Venn, pyramid/funnel, treemap and marimekko, heatmap, bar and dumbbell, waterfall, line (slopegraph, ridgeline, streamgraph, bump), Gantt and scatter charts (bubble, beeswarm), high-level, process, medallion, data flow, DP integration, DP security matrix, Sankey, fishbone, Wardley map, kanban, user journey, deployment, dependency graph, UML class, story map, or database schema diagrams as HTML/SVG/PNG, with .drawio, Mermaid, and .excalidraw import, plus lifecycle phase maps, block decomposition trees, and onboarding guidance.

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