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Use when designing the study for an Accounting, Organizations and Society (AOS) manuscript — qualitative field studies (access, case logic, interviews, observation), behavioral experiments, surveys, historical/archival inquiry, or theory-laden archival designs, each with the ethics and site-anonymity groundwork done early. Designs the inquiry; it does not run the coding or estimation (aos-data-analysis).
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Use when the research design and method are the bottleneck for an Academy of Management Journal (AMJ) manuscript — matching design (archival, survey, experiment, multi-method, field) and level of analysis to the theoretical question. Designs the study; it does not run the estimation or validity checks (amj-data-analysis).
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Estimates Fabric capacity cost before a migration by profiling Spark, SQL, Power BI, and Real-Time workloads, then recommending SKU size and comparing Reserved, Pay-As-You-Go, and Autoscale billing. Use only for capacity sizing and pricing questions, not for general migration or connectivity work.
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Build motor control solutions using Motor Control Blockset for PMSM, induction motors, BLDC, and SynRM. Implement field oriented control, sensorless FOC, six-step control, speed control, current control, and torque control. Configure SVPWM, flux weakening, MTPA, MTPV, control of non-linear motors, inverter control, and motor parameter estimation. Compose motor drive models, tune gains, and generate embedded code.
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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.
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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.
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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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Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-stabilizing transforms (logicle/biexponential, arcsinh, log) for flow and mass cytometry. Covers spillover-matrix estimation from single-stain controls, AutoSpill, the spillover spreading matrix and why panel design (not compensation) bounds resolution, compensate-then-transform ordering, and arcsinh cofactor choice (5 for CyTOF, ~150 for fluorescence, per-channel via flowVS). Use when correcting spectral overlap, preparing data for gating/clustering, choosing logicle vs arcsinh, deciding a cofactor, or distinguishing compensation from spectral unmixing.
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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.
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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.
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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.
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Integrate antennas into RF systems using MATLAB Antenna Toolbox and RF Toolbox. Covers impedance matching network design (L/Pi/Tee topologies, evaluation parameters, Richards transformation), measured antenna creation (E-field, directivity-only, EmbeddedE, ffsReader import), RF propagation and site planning (txsite/rxsite, coverage, SINR, ray tracing, link budget), and SAR estimation (birdcage+Phantom, conformalArray+Custom3D, direct EHfields). Use when the user wants to match an antenna, create a measuredAntenna, compute coverage or signal strength, perform ray tracing, or estimate SAR.
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Extract battery features for degradation analysis and health monitoring in MATLAB. Covers cycling test features, differential curves (IC/DV/DT), and measurement statistics. Use when working with battery cycling data, SOH estimation, RUL prediction, or any battery test data analysis in MATLAB. Triggers on battery* functions such as batteryTestDataParser, batteryTestFeatureExtractor, batteryMeasurementFeatures, batteryDifferentialCurves.
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Creates MATLAB interfaces to Python image processing and computer vision models from GitHub repositories or pip-installable packages using MPyReq. Use when asked to interface MATLAB with a Python CV/image model (segmentation, depth estimation, object detection, image generation, super-resolution, etc.), given a GitHub repo URL for an image/vision model, or asked to create an MPyReq demo for a deep-learning vision pipeline. Do NOT use for general-purpose Python-MATLAB interfacing, non-vision models (NLP, tabular, audio), model deployment/serving, or MATLAB-only image processing workflows.
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Run the measurement and ceremony layer of a delivery team: the metric set, estimation and capacity, the five sprint ceremonies, and the sprint report and quarterly rollup. Use this skill whenever the user is acting as PMO or scrum lead, planning a sprint, running standup, refinement, review, or retro, measuring velocity, cycle time, or throughput, checking capacity, or reporting on how a team is doing. Triggers on PMO, sprint planning, plan the sprint, standup, refinement, backlog grooming, sprint review, retro, velocity, capacity, cycle time, lead time, throughput, WIP, burndown, carryover, sprint report, story points to hours, how is the team doing, delivery metrics, agent lanes. Also triggers when the user asks how much work fits in a sprint or whether a team is on track, even if they never say sprint or PMO.
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Running experiments out of the data warehouse instead of via dedicated experiment platforms. SQL-based assignment, exposure logging discipline, metric definitions in dbt models, statistical analysis in SQL or Python, variance reduction with CUPED, sequential testing, and the operational tradeoffs vs platforms like Statsig and Optimizely. Triggers on warehouse-native experimentation, run experiments in BigQuery, run experiments in Snowflake, dbt experiments, SQL t-test, CUPED variance reduction, exposure log, sample ratio mismatch, sequential testing, mSPRT, doubly robust estimation, build vs buy experimentation. Also triggers when the team is choosing between platform and warehouse, building warehouse-native experiment infrastructure, auditing one, or running an experiment with a custom metric the platform cannot handle.
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Sequence an understood outcome into verifiable delivery slices with dependencies, ownership and acceptance checks. Use for delivery planning, estimation or migration strategy.
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Effort breakdown and estimation
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Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more
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Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
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Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
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Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA o
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Amazon negative keyword management and optimization. Search term analysis, waste reduction, savings estimation, and automated negative keyword strategies. Use when the user asks about negative keywords, search term analysis, ad waste reduction, or PPC optimization.
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Amazon FBA and FBM shipping cost calculator and fulfillment optimization. Dimensional weight analysis, storage fee calculation, removal cost estimation, and fulfillment method comparison. Use when the user asks about Amazon shipping costs, FBA fees, fulfillment costs, storage fees, or shipping calculations.
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