「analyzing」の検索結果

Processes environmental DNA metabarcoding data from raw amplicon reads to species occurrence tables using OBITools3, DADA2, and taxonomic assignment against BOLD, MIDORI2, or MitoFish databases. Handles COI, 12S, rbcL, and ITS barcode regions with primer removal, denoising, chimera detection, and contamination filtering via decontam. Includes occupancy modeling (occumb) for detection probability correction. Use when analyzing eDNA from water, soil, or bulk samples for biodiversity monitoring. Not for 16S human microbiome (see microbiome/amplicon-processing).

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Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.

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End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, choosing the correct hit-calling method by experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.

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Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.

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Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.

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Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.

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Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing risks via Fine-Gray vs cause-specific Cox, weighted log-rank and MaxCombo for non-proportional hazards, recurrent events (Andersen-Gill, PWP, WLW), and interval-censored data. Use when analyzing time-to-event endpoints (OS, PFS, DOR, TTR, TTNT) in oncology or other clinical trials.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.

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ESM2 protein language model for sequence scoring, embeddings, and plausibility checks. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai1-structure-prediction or boltz-structure-prediction. For QC thresholds, use protein-design-qc.

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ESM2 protein language model for embeddings and sequence scoring. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai or boltz. For QC thresholds, use protein-qc.

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Use this skill when working with RenderDoc capture files (.rdc), analyzing GPU frames, tracing shaders, inspecting draw calls, or running CI assertions against GPU captures. Trigger phrases: "open capture", "rdc file", ".rdc", "renderdoc", "shader debug", "pixel trace", "draw calls", "GPU frame", "assert pixel", "export render target".

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Map the competitive landscape before positioning your product for PRD v0.2 Market Definition. Triggers on completing v0.1 Spark, analyzing competitors, researching market, or requests like "competitive analysis", "who else solves this", "market landscape", "what alternatives exist", "competitor research", "feature comparison". Outputs CFD- entries for competitive intelligence and BR- entries for positioning rules.

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Understand essential business finance — profit margins, unit economics, cash flow, LTV/CAC, and the 4 methods to increase revenue. Use when: analyzing business profitability, making pricing decisions, evaluating SaaS unit economics, financial planning.

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Parse architectural drawings, floor plans, and building code compliance documents using Vision AI. Extracts building type, occupancy, floor areas, room layouts, dimensions, and code parameters. Use when: reading PDF floor plans, analyzing architectural drawings, extracting building data from images or scanned documents.

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Comprehensive content marketing toolkit with brand voice analysis, SEO optimization scripts, content frameworks, social media strategy, and content calendar planning. Use when writing blog posts, creating social media content, analyzing brand voice, optimizing SEO, planning content calendars, or developing content strategy. For deep SEO writing optimization, see the seo-content-writer skill.

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Use when computing orbits, planning maneuvers, propagating trajectories, or analyzing orbital perturbations for spacecraft or celestial bodies. Use when "orbit, trajectory, maneuver, delta-v, Hohmann, Keplerian, perturbation, J2, TLE, orbital elements, semi-major axis, eccentricity, inclination, RAAN, spacecraft propagation, Lambert solver, interplanetary, " mentioned.

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Use when designing space missions, computing launch windows, optimizing trajectories, analyzing payload constraints, or planning mission phases and contingencies. Use when "mission design, launch window, trajectory optimization, mission timeline, mass budget, propellant budget, mission phases, porkchop plot, C3, gravity assist, low thrust, mission architecture, LEO, GEO, interplanetary, " mentioned.

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Use when drafting patent applications, writing claims, analyzing prior art, or responding to office actions - covers USPTO practice, claim strategies, and specification requirementsUse when ", " mentioned.

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Use when designing ground station networks, scheduling satellite contacts, processing telemetry, commanding spacecraft, or analyzing link budgets. Use when "ground station, satellite contact, pass prediction, AOS, LOS, telemetry, commanding, uplink, downlink, antenna tracking, link budget, G/T, EIRP, " mentioned.

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Patterns for designing and analyzing clinical trials, including survival analysis, endpoint selection, sample size calculation, interim analyses, and regulatory considerations. Covers FDA/EMA guidelines and modern adaptive designs. Use when ", " mentioned.

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Use when building trading systems, backtesting strategies, implementing execution algorithms, or analyzing market microstructure - covers strategy development, risk management, and production deploymentUse when ", " mentioned.

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The practice of collecting, analyzing, and acting on data to drive product decisions. Great analytics isn't about dashboards—it's about insights that lead to action. Every metric should answer a question that changes behavior. This skill covers event tracking, metrics design, dashboards, user behavior analysis, and data-driven decision making. The best analytics teams measure what matters, not what's easy to measure. Use when "analytics, metrics, tracking, dashboard, funnel, cohort, retention, events, KPI, measure, data, insights, conversion, engagement, analytics, metrics, data, dashboards, tracking, funnels, cohorts, KPIs, insights" mentioned.

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Architecture Decision Framework workflow skill. Use this skill when the user needs Architectural decision-making framework. Requirements analysis, trade-off evaluation, ADR documentation. Use when making architecture decisions or analyzing system design and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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