490 件 ・ 関連度順
概要と使いどころ
Use when building the exhibits of an Accounting, Organizations and Society (AOS) manuscript — data-inventory and evidence tables for qualitative work, cell-means and process-test tables for experiments, and figures that carry theoretical weight — in Elsevier-compatible format. Builds exhibits; it does not run the analysis (aos-data-analysis).
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Use when planning an AAMAS project timeline from venue fit through abstract, full-paper or extended-abstract upload, supplementary material, the double-blind rebuttal, decision, IFAAMAS camera-ready, registration, and presentation, with track-specific deadlines and backward-planning offsets for a game-theory-plus-experiments paper.
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Use when revising an AAMAS paper so the interaction contribution leads the first page, the solution concept or incentive property is named, the game and agents are legible, claims are paired with proofs or multiagent experiments, the argument fits eight two-column pages plus references, and the wording stays double-blind.
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Use when running and reporting the statistical analysis for an Academy of Management Journal (AMJ) manuscript — measurement validity, common-method bias, the right estimator (HLM, SEM, panel, experiments), endogeneity, and robustness. Executes and reports the analysis; it does not design the study (amj-methods) or frame the contribution (amj-contribution-framing).
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Use when stress-testing the LOGIC of an Academy of Management Review (AMR) theory manuscript — checking logical coherence, running thought experiments and counterfactuals, addressing alternative explanations and disconfirming cases, and verifying each proposition follows from its argument. This is ARGUMENT DEVELOPMENT, NOT data analysis; AMR publishes no datasets, no statistics, and no empirical results.
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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.
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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.
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Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the critique that "n=3" is a publication convention rather than a power calculation. Use when budgeting a sequencing experiment, writing the sample-size justification in a grant, estimating replicates from pilot data, allocating a fixed budget between samples and depth, or planning scRNA-seq cohort size. For clinical-trial sample size see clinical-biostatistics/power-and-sample-size; for the power-given-n direction see experimental-design/power-analysis.
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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.
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Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.
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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.
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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.
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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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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.
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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.
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Design, validate, and plan a startup from scratch. Covers market research, competitive analysis, business model, brand identity, product definition, financial projections, and validation experiments. Trigger when the user has a startup idea to explore, wants to validate a business concept, needs a business plan or lean canvas, asks for market sizing or competitive landscape, wants brand positioning or go-to-market strategy, or says anything like "I have an idea for..." or "is this idea worth pursuing". Also handles resuming from a previous checkpoint.
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Evaluate ecommerce price candidates using unit economics, historical observations, elasticity analysis, scenario modeling, and controlled experiments. Use when a seller asks what price to test, how price changes could affect contribution or revenue, how to estimate elasticity, how to optimize a bundle or tier, or how to design a price experiment across Amazon, Shopify, TikTok Shop, Walmart, eBay, or other channels. Do not claim a proven optimal price without sufficient clean data, and do not change live prices without explicit authorization.
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Run conversion rate optimization through hypothesis-driven testing including audit, hypothesis generation, test design, statistical analysis, and rollout decisions. Use this skill whenever the user wants to optimize conversion, run A/B tests, audit a funnel, generate test hypotheses, design experiments, or analyze test results. Triggers on conversion optimization, CRO, A/B test, split test, multivariate test, hypothesis, conversion funnel, funnel audit, experiment design, statistical significance, lift, optimization. Also triggers when the user has a conversion problem and isn't sure where to start, or when test results are ambiguous and need interpretation.
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A platform decision framework for experimentation. When to use Statsig vs PostHog vs GrowthBook vs Optimizely vs Amplitude vs Eppo vs Kameleoon. How to migrate between them. How to coordinate when multi-platform is genuinely warranted. The decisions that compound for years and the ones you can defer. Triggers on which experimentation platform, choose Statsig vs PostHog, evaluate experimentation tools, switch experimentation platform, migrate from Optimizely, consolidate experimentation tools, multi-platform experimentation, experimentation platform decision, ab test platform selection, feature flag platform vs experiment platform, warehouse-native experiments, vendor lock-in experimentation. Also triggers when a team is asking about cost, governance, or migration cost across experimentation tools, or when an evaluation is starting.
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A discipline for designing experiments (A/B tests, multivariate, holdouts) so the results actually answer the question you asked. Hypothesis writing, sample size, duration, segment analysis, running discipline, matching a result to a pre-committed decision rule, and the common failure modes that produce confidently wrong shipping decisions. Use this skill whenever the user is planning a test that has not run yet: framing a hypothesis, sizing the sample, setting duration, choosing guardrails, or deciding whether something is worth testing at all. Triggers on design an experiment, experiment plan, A/B test, split test, multivariate test, holdout, experiment hypothesis, sample size, minimum detectable effect, MDE, test duration, guardrail metric, no peeking, pre-committed decision rule, is this worth testing. Use `experimentation-analytics` instead when the test has already run and the question is how to read the result panel.
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Designs chaos experiments, creates failure injection frameworks, and facilitates game day exercises for distributed systems with runbooks, experiment manifests, and rollback procedures.
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Growth marketing covering experimentation, funnel optimization, acquisition channels, retention, and viral growth. Use when designing A/B experiments, optimizing AARRR funnel stages, or prioritizing channels by CAC and LTV.
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Design and analyze A/B tests: sample size, test duration, and statistical significance for conversion experiments. Use when setting up an A/B test, calculating sample size, designing an experiment, or analyzing results.
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Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordina
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