「sequence analysis」の検索結果

ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.

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Conjecture generation, sequence analysis, and experimental mathematics for mathematical discovery. Covers sequence analysis (OEIS lookups, recurrence relations, generating functions), pattern detection methods (finite differences, ratio analysis, modular patterns), conjecture generation workflow, classical integer sequences (Fibonacci, Catalan, partition numbers, Bernoulli numbers), combinatorial identities, the probabilistic method (Erdos, expected value arguments, Lovasz Local Lemma), AI-assisted discovery (FunSearch, Ramanujan Machine), and confidence calibration with cautionary tales (Mertens conjecture, Polya conjecture). Use when discovering patterns, analyzing sequences, generating conjectures, or working with combinatorial identities.

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Analyze DNA/RNA/protein sequences. Use when the user provides a sequence and asks for analysis, translation, GC content, ORFs, motifs, restriction sites, or primer design. Triggers on "sequence", "translate", "GC content", "ORF", "primer", "restriction", "complement", "reverse complement".

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Expert-level bioinformatics covering sequence analysis, structural bioinformatics, database searching, phylogenetic analysis, NGS data processing, single-cell analysis, and machine learning in biology.

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Build accretion/dilution analysis for M&A transactions. Models pro forma EPS impact, synergy sensitivities, and purchase price allocation. Use when evaluating a potential acquisition, preparing merger consequences analysis for a pitch, or advising on deal terms. Triggers on "merger model", "accretion dilution", "M&A model", "pro forma EPS", "merger consequences", or "deal impact analysis".

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Restructure existing code without changing its behavior, through a test-gated refactoring loop: a named target, a green suite over that target before any edit, a planned sequence of small named refactorings, and the full suite re-run after every step. Use when the user wants to refactor, restructure, clean up, simplify, or improve the design of existing code, or to apply refactoring recommendations from a code-review or architectural-analysis report. This skill changes code; it does not review code (use code-review), assess architecture (use architectural-analysis), plan a multi-module restructure before executing it (use plan-a-change), map domain boundaries before restructuring along them (use ddd-analysis), or build new behavior test-first (use tdd). Do not use it on code inside an active tdd loop; the refactor step of tdd owns that cleanup. Runs its planned sequence to completion without pausing for review; to review each named refactoring as it lands, use pairing.

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End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comprehensive splicing analysis from raw bulk RNA-seq data; for variant-driven splice prediction see splice-variant-prediction; for rare-disease single-patient outlier detection see outlier-splicing-detection; for full-isoform PacBio/ONT analysis see long-read-splicing.

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工場の設備・人員・材料・納期を踏まえて生産順序を組み、段取り替えや工程間の負荷を調整し、設備故障や材料不足時の計画見直しを支援するスキル。

• 限られた設備での生産順序の検討
• 設備故障後に計画を組み直したいとき
• ロット量と段取り替え費用の比較

Analyzes the downstream impact (blast radius) using data lineage on Google Cloud when a BigQuery table or view is broken, stale, or modified. Identifies all downstream tables, dashboards, and processes that will be affected. Use when: - Performing a blast radius or impact analysis for a BigQuery table or view. - Assessing the consequences of modifying, deleting, or pausing updates to a BigQuery asset. - Identifying downstream dependencies (tables, dashboards, processes) of a BigQuery asset. Don't use for: - General BigQuery querying or data analysis (use BigQuery-related tools instead). - Non-BigQuery assets (e.g., Cloud Storage files) unless they are part of the BigQuery lineage. - Creating or modifying lineage links directly.

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Runs a sequenced monolith-to-modular pipeline that sizes and inventories components, finds shared domain duplication, addresses flattening and hierarchy issues, analyzes coupling, then groups components into candidate domain-aligned units, with optional embedded DDD strategic analysis for bounded contexts. Use when asking how to split a monolith, size components before extraction, find duplicated domain logic, clean up module hierarchy, measure coupling between modules, or group components into services. Do NOT use for phased extraction roadmaps or prioritization without the prior analysis steps (use decomposition-planning-roadmap after this pipeline), end-to-end legacy migration strategy writeups (use legacy-migration-planner), pure infrastructure capacity sizing, or when you only need DDD without the structural pipeline (install domain-analysis standalone).

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.

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Scene and sequence craft (场景/段落/细节/道具/悬念/情趣) — merged from Robert McKee's scene design and five-step scene analysis (value turn, beats, text/subtext, turning points, pacing, image systems), McKee's Dialogue scene types (balanced, comic, asymmetric, indirect, reflexive, minimal), Syd Field's sequence and scene elements, Neill Hicks (less is more, enter late leave early, energy), Richard Walter (action over talk, small gestures, avoid phones/cars/restaurants, list twelve alternative locations), Wendy Henson (action paragraphs, transitions, story-doing), Julian Hoxter (scene beats, objectives and tactics), Mei Feng's value test, and Lu Jun's chapters 意趣要足 (suspense, delay, wit), 细节要妙, 道具要精, 场景要当. Use when writing or fixing a single scene, choosing a location, building a sequence, planting a prop or detail, designing suspense and delay, cutting a scene that "nothing happens" in, or turning talk into action.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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Methodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence, image, spectral, structural, omics), quality assessment, report generation, format detection across 200+ formats. Use when given a data file for initial exploration or to pick an analysis before a pipeline.

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Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines. For PCR/restriction/cloning use biopython-molecular-biology; for SAM/BAM use pysam.

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Splits a body of context into a sequence of vertical-slice build phases where each phase is independently demonstrable to a real user and each builds on the previous. Use when the user wants to plan, sequence, phase, slice, break down, or order the build of a feature, capability, system, or initiative, and produces a plain-language phased build outline. Does not produce implementation detail — use plan-implementation. Does not specify behavior that has not been decided — use plan-a-feature. Does not perform gap analysis between two artifacts — use gap-analysis. Does not break a plan into independently-grabbable work items — use plan-work-items.

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Generate draw.io editable diagrams (.drawio, .drawio.svg) from text, images, or Excel. Orchestrates 3-agent workflow (Analysis → Manifest → SVG generation) with quality gates. Use when creating architecture diagrams, flowcharts, sequence diagrams, or converting existing images to editable format. Supports Azure/AWS cloud icons. Triggers on draw.io, drawio, ダイアグラム, アーキ図, フローチャート, シーケンス図.

Analyzes the downstream impact (blast radius) when a BigQuery table or view is broken, stale, or modified. Identifies all downstream tables, dashboards, and processes that will be affected. Use when: - Performing a blast radius or impact analysis for a BigQuery table or view. - Assessing the consequences of modifying, deleting, or pausing updates to a BigQuery asset. - Identifying downstream dependencies (tables, dashboards, processes) of a BigQuery asset. Don't use for: - General BigQuery querying or data analysis (use BigQuery-related tools instead). - Non-BigQuery assets (e.g., Cloud Storage files) unless they are part of the BigQuery lineage. - Creating or modifying lineage links directly.

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。

Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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。

Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Expert-level real analysis knowledge. Use when working with limits, continuity, differentiability, Riemann and Lebesgue integration, sequences and series of functions, metric spaces, measure theory, or functional analysis foundations. Also use when the user mentions 'epsilon-delta', 'uniform continuity', 'uniform convergence', 'Lebesgue integral', 'measure theory', 'sigma-algebra', 'Banach space', 'Hilbert space', 'completeness', 'compactness', 'Heine-Borel', or 'dominated convergence'.

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。

Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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。