「dna」の検索結果

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller. Distinguishes de novo CALLING (scanning a panel for unknown variants, bounded by per-locus error and multiple testing) from tumor-informed DETECTION (tracking a pre-specified variant set, where panel integration reaches single-ppm). Covers VarDict and Mutect2 for de novo calling, UMI-aware callers, and a pysam-based known-variant VAF tracker, with matched-WBC subtraction as the mandatory defense against clonal hematopoiesis (the dominant false positive). Use when calling or tracking tumor mutations from plasma cfDNA, setting a VAF threshold, or deciding whether a low-VAF call is tumor versus CHIP.

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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Specialized skill for nondominium Holochain DNA development, focusing on zome creation, entry patterns, integrity/coordinator architecture, ValueFlows compliance, and WASM optimization. Use when creating new zomes, implementing entry types, or modifying Holochain DNA code.

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Design DNA capture — extracts palette, type stack, motifs, motion, and 3D signatures from a shipped HTML file and saves them as a reusable reference pack. Use when the user says /reimagine-it lock, "lock this design", "save design DNA", "capture this look", or wants to reuse a shipped design on a different target. Locks capture palette, type, motif, and motion from a shipped HTML file. Part of the reimagine-it Content-Derived Design suite.

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Think and work like an expert Molecular Ecologist. Use when a task calls for Molecular Ecologist judgment. Reasons from population genetics, eDNA/metabarcoding, and marker choice (microsatellites, SNPs, mtDNA); analyzes with STRUCTURE/ADMIXTURE, hierfstat FST, DADA2 pipelines, and ddPCR; treats null alleles, Wahlund effect, batch effects, and eDNA allelic dropout as first-class failure modes.

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End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal, denoising with OBITools3 or DADA2, contamination filtering, taxonomy assignment, Hill number diversity, and constrained ordination. Use when processing environmental DNA samples for biodiversity assessment or ecological surveys.

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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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Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor mutations from plasma DNA or tracking specific variants.

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Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under peaks, query ENCODE cCREs or TF rPeak clusters from UCSC, check what tracks are available for a genome assembly, get chromatin accessibility across cell types, or cross-reference ENCODE data with UCSC-hosted annotations. Also use when the user mentions UCSC, genome browser, cCRE lookup, SCREEN, TF binding clusters, DNA sequence retrieval, or track data extraction.

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。

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller. Distinguishes de novo CALLING (scanning a panel for unknown variants, bounded by per-locus error and multiple testing) from tumor-informed DETECTION (tracking a pre-specified variant set, where panel integration reaches single-ppm). Covers VarDict and Mutect2 for de novo calling, UMI-aware callers, and a pysam-based known-variant VAF tracker, with matched-WBC subtraction as the mandatory defense against clonal hematopoiesis (the dominant false positive). Use when calling or tracking tumor mutations from plasma cfDNA, setting a VAF threshold, or deciding whether a low-VAF call is tumor versus CHIP.

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。

End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as screening-not-classifier (Davis 2018), tag-jumping with NovaSeq 10x MiSeq caveat (Schnell 2015), Hill-number effective species counts with coverage-based rarefaction (Jost 2006; Chao & Jost 2012; doubling rule), beta-diversity decomposition with MANDATORY PERMANOVA + PERMDISP pair (Anderson & Walsh 2013), constrained ordination, and the read-counts-not-abundance critique (Lamb 2019). Use when processing eDNA samples for biodiversity assessment, deciding ASV vs OTU, configuring OBITools3 v3, interpreting decontam screening, or reporting community comparisons with the dispersion confound check.

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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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。

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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。

张一鸣（字节跳动/TikTok创始人）的思维框架与表达方式。基于6个维度（著作、深度访谈、 表达DNA、他者视角、决策记录、时间线）的调研，涵盖32个访谈片段、12个重大决策案例， 提炼5个核心心智模型、7条决策启发式和完整的表达DNA。 用途：作为思维顾问，用张一鸣的视角分析产品、组织、全球化、人才和个人成长问题。 当用户提到「用张一鸣的视角」「张一鸣会怎么看」「一鸣的思路」「zhang yiming perspective」时使用。 即使用户只是说「帮我用张一鸣的角度想想」「如果是字节会怎么做」「切换到张一鸣」也应触发。 即使用户说「字节怎么看」「头条的逻辑」「一鸣怎么选择」「一鸣」也应触发。

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孙宇晨（Justin Sun / 孙割）的思维框架与行为逻辑。基于6个维度（著作、深度采访、表达DNA、 他者视角、决策记录、时间线）共1500+行调研素材的深度蒸馏， 提炼6个核心心智模型、8条决策启发式、5种割味造句公式和完整的表达DNA。 用途：作为思维顾问，用孙宇晨的视角分析营销策略、注意力经济、危机公关、叙事操控、蹭热点方法论。 割味十足的角色扮演——自大、暴论、碰瓷、数字轰炸、成功学底色。 当用户提到「用孙宇晨的视角」「孙割会怎么做」「孙宇晨模式」「Justin Sun perspective」「割神」时使用。 即使用户只是说「帮我用孙割的角度想想」「如果孙宇晨会怎么操作」「切换到割神」「用割的视角」也应触发。

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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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Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.

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Dispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.

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Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.

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Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1) Computing per-nucleotide or per-sequence likelihoods for variant effect scoring, (2) Embedding genomic windows for downstream classification, (3) Generating DNA conditioned on a prefix, (4) Scoring regulatory or coding regions across species.

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DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

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Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice. Use for Evo2/Evo 2, DNA generation, genomic sequence generation, hosted generation, local Docker deployment, local forward passes, layer outputs, logits, sampled probabilities, and BioNeMo NIM workflows.

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。

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.

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Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline, SQANTI3, and ONT tools (IsoQuant, FLAIR, Bambu, StringTie2). Covers why a novel isoform is an artifact until proven otherwise (RT template-switching, intra-priming, and 5' degradation manufacture junctions and truncations), the SQANTI3 structural categories and their trust order, the Kinnex skera-split step, orthogonal CAGE/poly-A/short-read-junction validation, and why long-read isoform quantification needs EM. Use when building a full-length isoform catalog, classifying/filtering long-read transcripts, running Iso-Seq or ONT cDNA/dRNA analysis, or judging novel-isoform reliability.

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。