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概要と使いどころ
Use when the theoretical puzzle is the bottleneck for an Academy of Management Review (AMR) manuscript — deciding whether an idea is theory-worthy and AMR-fit before any theorizing begins. Frames the puzzle; it does NOT build constructs (that is amr-theory-development) or design any empirical study (AMR has none).
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Use when deciding whether a project fits ACL versus EMNLP, NAACL, EACL, TACL, Computational Linguistics, COLM, or an ML venue, covering contribution typing for NLP work, long-versus-short paper choice, the annual theme track, Findings-tier expectations, and sharpening the computational-linguistics framing before writing starts.
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 planning an ACL project calendar across ACL Rolling Review cycles, covering cycle selection against conference commitment windows, backward planning from an ARR deadline, the review-response-meta-review timeline, commitment decisions, resubmission loops to later cycles, and camera-ready through ACL Anthology publication.
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 deciding whether a project is a strong AAAI submission across its broad AI scope, should be reframed or routed to a dedicated track such as AI for Social Impact or AI Alignment, or should instead go to IJCAI, NeurIPS, ICML, ICLR, AISTATS, UAI, ACL, CVPR, KDD, CHI, ICRA, or another specialist venue.
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 deciding which amann-* sub-skill to invoke next, or when sequencing a comprehensive review article from topic selection through revision for an Academy of Management Annals (Annals) submission. Routes — it does not replace — the specialized skills.
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 scoping or sanity-checking a research question for an Academy of Management Journal (AMJ) manuscript — fit, theory-drivenness, and feasibility. Decides whether the idea can earn a theoretical contribution; it does not build the theory itself (use amj-theory-development) or position the literature (amj-literature-positioning).
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 deciding whether a project is a strong AAMAS fit, comparing AAMAS with AAAI, IJCAI, NeurIPS, ICML, EC, and the JAAMAS journal, identifying whether the agents are truly the research object, naming the interaction primitive (solution concept, mechanism, coordination, negotiation), and sharpening the multiagent framing before writing begins.
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 judging whether a management/organization literature is an Academy of Management Annals (Annals)-scale review topic — mature, important, fragmented, and integrable into a new framework — rather than a narrow review. Decides fit and frames the review's animating problem; it does not gather the literature (amann-literature-synthesis) or write the proposal (amann-proposal-framing).
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 deciding which amj-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an Academy of Management Journal (AMJ) manuscript. Routes — it does not replace — the specialized skills.
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 planning an AAAI project timeline from topic selection through abstract, OpenReview submission, two-phase review, rebuttal, decision, camera-ready, registration, presentation, and public artifact release.
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 designing or auditing AAMAS experiments - self-play and population-based training, opponent selection, equilibrium and regret metrics, game-theoretic simulations, ablations, seeds, hyperparameters, compute, and claim-to-evidence fit - with emphasis on experiments that probe the interaction rather than chase a single-agent leaderboard.
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。
Compose screen and interaction traps: navigation, adaptive layout, window insets, pagers, toolbars, sheets, list drag and selection, sliders, text fields, settings UI, one-shot effects. Use when layout, gestures or navigation misbehave.
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。
Repurposes long-form video (podcasts, interviews, talks) into short-form vertical clips for Instagram Reels, TikTok, and YouTube Shorts. Handles transcription, moment selection, clip extraction, speaker-tracked reframing (16:9 to 9:16), and animated captions.
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。
Configure Simulink models for Embedded Coder (ERT), Simulink Coder (GRT rapid-prototyping), or AUTOSAR code generation. Use when the user asks to generate embedded C or C++ code, run a full build of a model, produce a code generation report, configure a model for production/ECU deployment or rapid-prototyping code, target ARM or x86 hardware, apply MISRA C/C++ compliance (ERT/AUTOSAR only — Simulink Coder does not ship MISRA profiles), or set up GRT, ERT, AUTOSAR, or shared-library targets. Handles target selection, hardware mapping, model hierarchy propagation, and constraint introspection via the configure_for_codegen function. Do NOT use for GRT shared-library variants (grt_malloc.tlc), DDS, or ROS, or for iterative optimization workflows that measure baseline metrics, apply targeted changes, and re-measure to confirm improvement.
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。
Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across samples until normalized, the CPM/RPKM/BPM/RPGC normalization menu and the conserved-total assumption that makes them wrong under a global perturbation, the strict sorted-non-overlapping-chrom.sizes bedGraphToBigWig contract that silently corrupts a bigWig, effective-genome-size selection, and bin-size aliasing. Use when building or normalizing a coverage/signal track from a BAM, comparing tracks across samples or conditions, converting bedGraph to a browser-ready bigWig, or diagnosing a track that looks plausible but reports wrong heights.
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。
Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.
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Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC locus tags. Covers Bakta-vs-Prokka-vs-PGAP-vs-DFAST choice, light-vs-full database tiers, translation-table selection (11/4/25), archaeal and leaderless-gene caveats, the small-ORF blind spot, pseudogene-vs-phase-variation, the pangenome re-annotation trap, and submission compliance. Use when annotating a newly assembled prokaryotic genome, choosing an annotation tool, re-annotating a collection for pangenomics, or preparing annotations for NCBI/DDBJ submission.
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Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.
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。
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.
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。
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.
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 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.
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。
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.
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。
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.
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 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.
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。