「analysis」の検索結果

Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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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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Process and generate multimedia content using Google Gemini API. Capabilities include analyze audio files (transcription with timestamps, summarization, speech understanding, music/sound analysis up to 9.5 hours), understand images (captioning, object detection, OCR, visual Q&A, segmentation), process videos (scene detection, Q&A, temporal analysis, YouTube URLs, up to 6 hours), extract from documents (PDF tables, forms, charts, diagrams, multi-page), generate images (text-to-image, editing, composition, refinement). Use when working with audio/video files, analyzing images or screenshots, processing PDF documents, extracting structured data from media, creating images from text prompts, or implementing multimodal AI features. Supports multiple models (Gemini 2.5/2.0) with context windows up to 2M tokens.

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Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

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Use when a problem requires structured step-by-step reasoning before acting. Prevents jumping to conclusions or guessing root causes without evidence. Triggers on complex debugging, multi-step analysis, hypothesis verification, or when mk:fix invokes diagnosis phase. NOT for being stuck on approach (too many implementations, forced assumptions, innovation block) — use mk:problem-solving instead.

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Use when a project has no docs/ directory or needs initial documentation generated from codebase analysis. Triggers on "init docs", "create documentation", "generate docs", "docs init", or when docs/ is empty. Do NOT use for updating existing docs (use mk:document-release).

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Structured second-pass reasoning after code review or plan evaluation. Offers named reasoning methods (pre-mortem, inversion, red team, Socratic, etc.) to re-examine findings through a specific lens. Use after /mk:review verdict or any time deeper analysis is needed on an existing output. NOT for initial review (see mk:review); NOT for creating implementation plans (see mk:plan-creator).

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Deep spec analysis on a Confluence page. Reads page (+ children) via the confluence-as wrapper, produces a structured Spec Research Report with requirements, acceptance criteria, gaps, ambiguities, and suggested user stories for human review. Read-only — does NOT create Jira tickets. Triggers: 'analyze spec for PAGE-ID', 'extract requirements from confluence page', 'spec research on URL'. NOT for raw page CRUD (mk:confluence-page); NOT for ticket complexity scoring (mk:planning-engine).

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Use this skill for ANY of the following — do not skip it even if the query seems simple: strategic decisions, business analysis, thesis building, complex problem solving, geopolitical analysis (non-market), philosophical reasoning, academic research, system design, decision under uncertainty, long-form thinking, or any question that benefits from First Principle deconstruction and multi-agent reasoning. ALWAYS use this skill when the user asks about: why something works the way it does, whether a decision is correct, how to think about a complex problem, what could go wrong, analyzing a situation from multiple angles, or any "should I..." question involving real-world trade-offs. This is NOT a market/trading skill — for financial markets, BTC, gold, stocks, forex, macro economics, use money-atlas-intelligence-os instead.

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Reddit compound content operations skill. Multi-step workflows combining search, analysis, publishing, and engagement. Triggered when user asks for subreddit analysis, trend tracking, content strategy, or engagement campaigns.

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Generalize published Spectre and remote microarchitectural research into passive target prerequisites, defensive review, and approval-gated local validation. Use for shared runtimes, JavaScript isolates, edge workers, serverless platforms, browser sandboxes, remote timing, cache side channels, speculative type confusion, or Dynamic Process Isolation analysis.

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Deep-dive framework for analyzing crypto tokens — market data, liquidity health, tokenomics, unlock schedules, and risk assessment. Combines on-chain data, API queries, and multi-source validation to generate actionable investment verdicts.

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Analyze credential pooling operations and API reseller business models — economics, risks, detection patterns, and sustainability

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Build image analysis applications with Azure AI Vision SDK for Java. Use when implementing image captioning, OCR text extraction, object detection, tagging, or smart cropping.

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Azure AI Vision Image Analysis SDK for captions, tags, objects, OCR, people detection, and smart cropping. Use for computer vision and image understanding tasks.

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Expert-level signal processing covering Fourier analysis, sampling theory, digital filters, FFT, spectral estimation, and adaptive filtering.

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Expert-level metals engineering covering crystal structure, phase diagrams, strengthening mechanisms, steel metallurgy, aluminum alloys, and failure analysis.

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Expert-level compiler design covering lexical analysis, parsing, semantic analysis, intermediate representations, optimization passes, and code generation.

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Expert-level mechanical vibrations covering free and forced vibration, damping, resonance, modal analysis, vibration isolation, and rotating machinery.

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Expert-level spacecraft design covering mission analysis, subsystem design, power and thermal management, attitude control, communications, and systems engineering.

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Expert-level biomechanics covering musculoskeletal mechanics, gait analysis, joint biomechanics, soft tissue mechanics, bone mechanics, and sports biomechanics.

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