「dna」の検索結果

GPS-aligned genealogical research assistant for family history, ancestor research, record analysis, source-information-evidence classification, conflict resolution, citations, FAN research, privacy-sensitive document analysis, and proof statements, summaries, or arguments. Use for census, vital, probate, land, military, church, newspaper, DNA-plus-documentary, and other genealogy evidence tasks. Not for GEDCOM creation (use gedcom-creator), general history questions, DNA-kit shopping, or generic writing tasks.

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Use when the user says 'analyze my wordpress site', 'what is running on my site', 'site dna', or 'what plugins are on my site'. Detects every page builder, audits active versus dead-weight plugins, maps content structure, finds orphaned shortcodes, and checks performance and security posture.

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。

Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is DNA methylated/unmethylated in my tissue?" by combining per-CpG methylation data into tissue-level methylation profiles. Handles coverage filtering, identifies hypomethylated regions (HMRs) and partially methylated domains (PMDs), and manages cross-lab variation.

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。

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak set. Handles cross-lab variation, ATAC vs DNase platform differences, and ENCODE blocklist filtering.

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。

DNA methylation analysis — array and bisulfite-seq processing, DMP/DMR calling, and epigenetic clocks.

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。

Extract a public-safe brand and offer profile for paid advertising from an authorized website and operator input. Triggers on: brand DNA, brand profile, brand identity, brand style, brand colors, brand voice, visual identity, style guide, website brand analysis.

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The GraphQL pipeline for SKMTC generators — authoring generators whose input schema is GraphQL SDL rather than OpenAPI. Covers `toGqlOperationEntry`, `GqlOperation`, `synthesizeArgsObject` (mutation args -> object schema), the GQL enrichment routing (`[id][rootKind][fieldName][variant]` — two nested subject keys where OAS has path+method), the `to<Lang>GqlOperationProjectionBase` companion factories, and the `GeneratorKey` shape `id|rootKind|fieldName|variant`. Use this skill ALONGSIDE `skmtc-generator` whenever the schema source is GraphQL SDL or the task mentions "GraphQL", "SDL", "GqlOperation", "toGqlOperationEntry", or GraphQL query/mutation generators. Engine rules (producers, register/insert, the axioms) stay in `skmtc-generator`; this skill carries only what differs for GraphQL.

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Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.

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Detects m6A modifications from Oxford Nanopore direct-RNA-seq (DRS) signal using m6Anet (multiple-instance-learning over DRACH 5-mer signal). Covers the upstream pipeline (Dorado/Guppy basecalling -> minimap2 map-ont -> nanopolish eventalign -> m6anet dataprep -> m6anet inference), per-site vs per-read probability including the mod_ratio stoichiometry column, the DRACH-only constraint, minimum-coverage thresholds (20-50 reads/site), multi-condition comparison via xPore/Nanocompore/ELIGOS, Dorado native modification calling (RNA004, 2024+), and the cDNA-vs-DRS distinction (cDNA Nanopore CANNOT detect modifications). Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting probability_modified vs mod_ratio vs per-read probabilities, deciding between m6Anet (known DRACH sites) and Dorado/Remora (genome-wide screening), pinning RNA002 vs RNA004 chemistry and basecaller versions, or troubleshooting eventalign/dataprep failures.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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。

Expert-level biochemistry knowledge. Use when working with proteins, enzymes, metabolism, DNA, RNA, carbohydrates, lipids, cell signaling, or bioenergetics. Also use when the user mentions 'enzyme kinetics', 'metabolism', 'glycolysis', 'Krebs cycle', 'DNA replication', 'protein folding', 'amino acids', 'ATP', 'oxidative phosphorylation', 'gene expression', 'lipid bilayer', or 'signal transduction'.

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。

Expert-level molecular biology knowledge. Use when working with DNA replication, transcription, translation, gene regulation, cloning, PCR, sequencing, CRISPR, epigenetics, or molecular techniques. Also use when the user mentions 'DNA replication', 'transcription', 'translation', 'gene expression', 'PCR', 'cloning', 'restriction enzyme', 'gel electrophoresis', 'Western blot', 'CRISPR', 'epigenetics', 'promoter', 'enhancer', or 'RNA splicing'.

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。

METAINFORMANT rules for directory src/metainformant/dna/annotation. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/alignment. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/expression. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/phylogeny. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/io. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/population. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/integration. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/sequence. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/external. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna/variation. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory src/metainformant/dna. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。

METAINFORMANT rules for directory scripts/dna. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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。