「structure」の検索結果

Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.

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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), 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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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

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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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Use this skill when the user asks how to recruit CDL drivers — sourcing channels (CDL schools, job boards, military, returning citizens, owner-operator pools), application + screening process, signing bonus structures, recruitment marketing, fleet ambassador programs, and what's working in the current driver market. Reference ATA Workforce Development.

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Use when a safety director, operations manager, or fleet owner asks for templates, topics, or structure for recurring safety meetings — weekly driver meetings, monthly safety committee meetings, quarterly all-hands safety reviews, or post-incident safety stand-downs.

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Use this skill when the user asks about team driving — two-driver OTR operations, how teams maximize miles, HOS rules with sleeper berth swap, pay structures, equipment requirements (sleeper berth specs), team retention, and common challenges. Reference 49 CFR 395.1(g).

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Use this skill when the user asks how to build, measure, or improve safety culture in a motor carrier — leading vs lagging safety indicators, blame-free reporting, near-miss programs, safety committee structure, monthly safety meetings, ATA Safety Management Program guidance, and how to evaluate cultural maturity. Reference ATA SMP + DOT safety culture research.

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Use when a carrier is evaluating ELD / telematics / dashcam platforms and needs an objective comparison of Samsara, Motive (formerly KeepTruckin), and Geotab. Covers ELD compliance, AI dashcams, driver scoring, integrations, pricing structure, and which fleet profile suits which platform.

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Use this skill when the user asks about FMCSA financial assistance + grants — Motor Carrier Safety Assistance Program (MCSAP), High Priority Grants, CMV Operator Apprenticeship Program (CMV-DAP), workforce development funding, hazmat preparedness grants, small carrier financial relief, and state-level grants for trucking infrastructure. Reference fmcsa.dot.gov/grants.

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Use when a carrier asks about electric trucks — Tesla Semi, Freightliner eCascadia, Volvo VNR Electric, Peterbilt 579EV, range, charging, total cost of ownership, regulatory pushes (CARB ACT, ACF), incentives, infrastructure, depot vs en-route charging, and which routes/applications are EV-ready today.

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Use when a manager, dispatcher, or safety director needs to have a coaching conversation with a driver — about a safety event (harsh brake, hard turn, distraction), an HOS violation, a customer complaint, a missed delivery, repeated minor incidents, or to deliver positive recognition. Covers conversation structure, language, documentation, and escalation.

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Use when a carrier owner, CFO, or controller asks how to build an annual budget, monthly P&L model, cash flow forecast, scenario plan, or break-even analysis for a trucking operation. Covers revenue modeling, cost structures, capital planning, and the discipline of tracking actuals vs budget.

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Use this skill when the user asks about carrier-driver relationships — Independent Contractor (IC / 1099) vs Employee (W-2), Owner-Operator lease agreements, the AB5 California law, the DOL 2024 IC test, lease-purchase programs from the carrier side, settlement statements, deductions, and how to structure a compliant IC arrangement. Cite 49 CFR 376 + 1099 IRS rules.

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Use this skill when the user asks about buying or selling a trucking company — valuation drivers (revenue, fleet age, CSA scores, customer concentration), asset purchase vs stock purchase, FMCSA authority transfer, due diligence checklist, common deal structures (cash, earnout, seller-financed), and what changes operationally after acquisition. Reference 49 CFR 365.401 (authority transfer).

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FIPA standard library of agent interaction protocols for structured multi-agent communication

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