Results for “selection”

Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 7.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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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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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Use when a carrier asks about tire program design, when to retread vs replace, position management (steer vs drive vs trailer), inflation pressure standards, casing management, scrub rates, road-call prevention, or vendor program selection (Bridgestone, Michelin, Continental, Goodyear). Covers 49 CFR 393.75 and DOT roadside out-of-service criteria.

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Use this skill when the user asks about International Fuel Tax Agreement (IFTA) compliance — quarterly returns, jurisdiction reporting, fuel + miles reconciliation, IFTA-100/101 forms, base jurisdiction selection, IFTA license + decals, recordkeeping requirements, common IFTA audit findings, or how to handle non-IFTA jurisdictions. Cite IFTA Articles of Agreement.

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Use this skill when selecting a Consortium/Third-Party Administrator (C/TPA) for drug + alcohol testing program management. Covers what services they provide, what to look for, and red flags.

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Use this skill when selecting an MRO for drug testing program oversight. Covers MRO qualifications under Part 40, what the MRO does, and how to evaluate MRO services.

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Use this skill when the user asks about commercial driver drug & alcohol testing under 49 CFR 382 + 40 — the six testing reasons (pre-employment, random, post-accident, reasonable suspicion, return-to-duty, follow-up), MRO process, SAP/return-to-duty process, post-accident triggers, random selection rates, what panels are tested, refusal definitions, or testing programs and consortiums. Cite specific 49 CFR 382 or 40 subsection.

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Use this skill when referring a driver to SAP after a positive test or refusal. Covers SAP selection, the evaluation/treatment cycle, return-to-duty test, and follow-up testing schedule.

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Use when a carrier asks about fuel-card vendor selection (Comdata, EFS, WEX, RTS, Pilot Flying J, Love's Connect), discount levels, fraud control, driver authorization PINs, IFTA reporting features, cash advance, money codes, or how the card fits into payroll/settlement workflows.

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Use this skill when the user asks about FMCSA Compliance Safety Accountability (CSA) program scoring — the seven BASIC categories, BASIC Severity Indicator (BSI), peer percentiles, intervention thresholds, how violations age out, SMS Methodology, ISS (Inspection Selection System), what "alert" status means, Safety Measurement System mechanics, or DataQ disputes. Cite SMS Methodology v3.20.

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Manage DAG execution lifecycles including start, stop, pause, resume, and cleanup. Activate on 'execution lifecycle', 'stop execution', 'abort DAG', 'graceful shutdown', 'kill process'. NOT for cost estimation, DAG building, or skill selection.

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An innate exploratory drive that guarantees no graph node remains permanently invisible to an agent population. After a warm-up period (step > 3), each agent fires a coverage scan with probability |unseen_nodes| / |all_nodes|. When triggered, the agent teleports directly to the globally unseen node with the highest belief uncertainty, works it, and returns control to the normal action-selection loop. Probability is self-annealing: it starts near 1.0 when almost everything is unseen and decays toward 0.0 as coverage saturates, requiring no manual schedule. The mechanism is "innate" (hard-coded into the agent step loop) as distinct from the "adaptive" EFE path, which requires local neighbors and learned precision weights. Together they form a two-layer exploration architecture: adaptive for locally-guided foraging, innate for topological completeness.

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Data structures and algorithms for AI agent episodic memory. Covers vector stores (HNSW, IVF, PQ), temporal indexing, knowledge graphs with triple stores, hierarchical summarization, forgetting curves, working/long-term/ procedural memory, and memory consolidation. Deep analysis of MemGPT/Letta, Zep/Graphiti, Mem0, and the Stanford generative agents memory architecture. Teaches the CS fundamentals behind how agents remember, retrieve, and forget. Activate on: "agent memory", "episodic memory", "vector search algorithm", "HNSW", "memory retrieval", "forgetting curve", "knowledge graph memory", "MemGPT", "Letta", "Zep", "Mem0", "memory consolidation", "temporal retrieval", "agent long-term memory", "memory layer". NOT for: conversation protocol design (use agent-conversation-protocols), agent infrastructure selection (use agentic-infrastructure-2026), building RAG pipelines (use ai-engineer).

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Frontend stack decisions, Cloudflare deployment patterns, component systems, and internal tools architecture. Use for framework selection, deployment strategy, design system bridging, shadcn setup. Activate on "frontend architecture", "tech stack", "Cloudflare Pages", "component library", "internal tools", "shadcn setup". NOT for writing CSS (use frontend-developer), design critique (use design-critic), or backend APIs.

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