2,349 件 ・ 関連度順
概要と使いどころ
Use when preparing the data, code, and model materials for an Agricultural Systems (AgSy) manuscript. AgSy applies Elsevier's research-data policy, which treats software, code, and models as research data — deposit them in a repository and cite/link them, or state why they cannot be shared. Covers model-description standards and exemptions. Prepares the materials; it does not waive requirements.
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Use when targeting Communications Earth & Environment or deciding whether an earth, environmental, or planetary-science manuscript fits this venue. Encodes the journal's fit, the solid-and-complete-advance bar, Nature Portfolio reporting/data standards, house style, official-submission re-check, and desk-reject heuristics.
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Use when building or revising exhibits for an American Economic Journal: Macroeconomics (AEJ: Macro) manuscript — impulse-response figures, fan charts, model-fit overlays, and regression/moment tables — to AEA house standards and macro conventions. Formatting and clarity; it does not generate the underlying estimates.
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Use when judging whether a manuscript's landing point is an ACCOUNTING issue (accounting information / disclosure / audit / standards) versus a corporate-finance mechanism, before drafting for 《会计研究》 (Accounting Research). Use this to decide fit and to re-route finance-mechanism papers to a finance journal before any other acr-* skill.
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Use when responding to 《会计研究》 (Accounting Research) reviewer reports / an R&R — drafting a point-by-point response letter and 修改说明 that addresses accounting-measure construction, institutional/standard accuracy, identification, and information-mechanism concerns, while keeping the revision anonymous. Use only after the manuscript itself has been revised.
日本語の概要は準備中です。原文の説明を表示しています。
Use when writing the contribution and implications section for a 《会计研究》 (Accounting Research) manuscript — articulating both the accounting-theory contribution (role of accounting information) and concrete implications for standard-setters, regulators, and audit/reporting practice. Use after results and tables are final.
日本語の概要は準備中です。原文の説明を表示しています。
Use when framing or sharpening a topic for 《会计研究》 (Accounting Research) — turning a generic "X affects Y" empirical idea into an accounting contribution anchored in China's institutional setting, accounting theory, and standard-setting / practice relevance. Use before literature review.
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Use when appraising the cumulative evidence and ensuring balance in an Academy of Management Annals (Annals) review — weighing conflicting findings by credibility, steelmanning rival schools, and handling the author's own work even-handedly. Audits evidence quality and fairness; it does not design the framework (amann-organizing-framework) or build exhibits (amann-tables-figures).
日本語の概要は準備中です。原文の説明を表示しています。
Use when building the novel integrative framework that an Academy of Management Annals (Annals) review must deliver — the theory-advancing "new way of seeing the field" that is the acceptance bar, not a catalog of papers. Designs the spine; it does not gather the literature (amann-literature-synthesis) or appraise evidence balance (amann-evidence-standards).
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Use this skill when the user asks to check Simulink model compliance against a standard (MISRA, MAB, JMAAB, ISO, DO, IEC, EN, CERT C/CWE, AUTOSAR, Simulink Code Inspector (SLCI)), wants to run Model Advisor checks, or needs a compliance report with fix suggestions. For JMAAB/MAB, supplement deterministic checks with agentic review of uncheckable guidelines.
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Author or upgrade Model Advisor checks for Simulink and System Composer models. Covers the full lifecycle: guideline authoring, check specification, Model Advisor check implementation, and qualification testing. Use when creating new checks (edit-time, standard batch, config-parameter, auto-fix), converting legacy StyleOne/StyleTwo/StyleThree checks to modern DetailStyle, creating a guideline for modeling, enforcing a modeling rule, or testing/qualifying a check. Triggers on any modeling constraint (e.g., "blocks shall...", "signals must match...", "parameters shall be set to...").
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Write modern, high-performance C# code using records, pattern matching, value objects, async/await, Span<T>/Memory<T>, and best-practice API design patterns. Emphasizes functional-style programming with C# 12+ features.
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Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.
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Phases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) with WhatsHap, LongPhase, or HiPhase, and haplotags the BAM (HP/PS tags) for allele-resolved downstream analysis. Covers why phase blocks break at het-sparse gaps (read length x heterozygosity), why phasing the VCF is useless until the BAM is haplotagged, the GT-pipe/PS and read HP/PS tag spec, reporting block N50 with switch error, the diploid-assumption/CNV/haploid-region traps, trio phasing as the gold standard, and the boundary to statistical panel phasing. Use when phasing long-read variants, haplotagging reads for allele-specific methylation/expression or phased SVs, choosing WhatsHap vs LongPhase vs HiPhase, trio phasing, or assessing phasing quality.
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Tracks ctDNA across serial liquid-biopsy timepoints for molecular residual disease (MRD) and treatment-response monitoring, treating MRD as a binary integrated detection call across the patient's full variant set (with a defined LoD95 and per-sample specificity) rather than a per-timepoint VAF threshold, and handling undetectable samples as left-censored at the per-sample limit of detection rather than true zeros. Covers tumor-informed bespoke vs tumor-naive design, landmark vs surveillance sampling, molecular-response definitions and their non-standardization, censoring-aware clearance kinetics, and the multiple-testing structure of repeated surveillance. Use when monitoring ctDNA during therapy, calling molecular relapse before imaging, or estimating clearance half-life from serial samples.
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Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.
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Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.
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Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.
日本語の概要は準備中です。原文の説明を表示しています。
Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).
日本語の概要は準備中です。原文の説明を表示しています。
Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).
日本語の概要は準備中です。原文の説明を表示しています。
Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and the n=3 visualization stake. Use when generating DE diagnostic plots, choosing VST vs rlog for visualization, troubleshooting suspicious plot patterns (shifted MA cloud, batch-dominated PCA, anti-conservative p-value histogram), or building a standard QC figure panel.
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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.
日本語の概要は準備中です。原文の説明を表示しています。