「fea」の検索結果

Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

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Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.

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Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.

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Guides the creation of complete Spring Boot features following a structured, layer-by-layer workflow: entity, repository, service, controller, and tests. Applies Kotlin idioms, Bean Validation, and MockK test patterns throughout.

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Run the full feature workflow — task validation, technical design, implementation, testing, review, and documentation.

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任意のタスク（GitHub Issue・自由記述リクエスト・口頭要件）を起点に、受け入れ条件確認・スコープ定義・影響分析・テスト戦略を含む実装計画（15セクション）と、builder エージェントへ渡す features.json を生成します。「〇〇を作って」「実装計画を作って」「Issue

features.json を読み込み、pending な機能を1件ずつ tdd-guide エージェント（内部で tdd-cycle を使用）で実装するスキル。 Context anxiety（トークン上限接近による焦り）と Context rot（情報劣化）を防ぐため、 機能単位のループ・状態管理・implementation-notes.md への記録を担う。 builder エージェントが実装フェーズを開始するときは必ずこのスキルを呼ぶ。

Planner→Builder→EvaluatorのLong-Runningエージェントハーネスで複雑なタスクを実装します。plannerがfeatures.jsonに機能を分解し、builderがTDDで1機能ずつ実装し、evaluatorがPASSするまでbuilderを繰り返します。「〇〇を作って」「実装して」「long-running」などのリクエストで起動します。

Extract study sites, observational variables, coordinates, climate-forcing sources, and cited data sources from ecosystem-modeling papers, PDFs, supplements, or article text, then plan or create EcoSIM simulation workflows and run folders for those sites. Use when Codex is asked to read a paper for EcoSIM feasibility, including requests phrased as "read paper for ecosim feasibility"; read a paper for sites/data availability; reproduce a published site simulation in EcoSIM; compare EcoSIM outputs to paper observations; or convert paper-derived AmeriFlux, FLUXNET, US NLDAS-domain, non-US ERA5, crop, peatland, forest, grassland, wetland, or unmanaged field-site information into EcoSIM inputs and runnable cases.

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Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.

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Master advanced AgentDB features including QUIC synchronization, multi-database management, custom distance metrics, hybrid search, and distributed systems integration. Use when building distributed AI systems, multi-agent coordination, or advanced vector search applications.

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Use when an approved PRD must become an executable roadmap — 'gerar roadmap do PRD', 'quebrar o PRD em épicos e features', 'cadeia de dependências', 'roadmap with dependencies' — Phase/Epic/Feature/Task with explicit dependencies, waves and critical path, validated by a deterministic checker, with an approval gate. Do NOT use for a PRD that is not approved (prd- create/prd-refine first).

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Use when the user, inside an Orca terminal, asks Hermes to resolve, dispatch, orchestrate or supervise GitHub issues with Orca workers — 'orquestrar as issues 12, 15 e 18 no Orca', 'despachar as issues com label ready', 'coordenar workers do Orca para estas issues', or to resume such a Run after compaction. Do NOT use for a single unsupervised hand-off to another agent (Orca CLI directly), for working on one issue in this session (pwdev-feat feat-loop), or outside Orca.

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Discover and approve feature requirements through focused interviewing and repository research. Use when the user has a feature idea, unclear scope, conflicting requirements, or needs Flow context artifacts before design.

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Segundo cérebro persistente em Markdown — LLM Wiki no padrão Karpathy mantida como bundle Open Knowledge Format v0.2, com fontes imutáveis em raw/ e conceitos citados em wiki/. Use quando o usuário disser "segundo cérebro", "second brain", "adiciona isso ao meu brain", "salva na minha wiki", "ingere esse artigo/PDF/link", "o que minha wiki diz sobre", "o que meu brain sabe sobre", "consulta meu conhecimento", "lint da wiki", ou pedir para acumular conhecimento de fontes de forma durável. NÃO use para notas do Obsidian (pwdev-obsidian), planejamento de features (pwdev-feat) nem PRDs (pwdev-prd).

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Implement real-time features using Convex reactive queries that automatically update when data changes, enabling live collaboration, instant updates, and reactive UIs without manual polling. Use when building live dashboards, implementing collaborative editing, creating chat applications, showing real-time notifications, building activity feeds, implementing presence indicators, creating reactive search, or any feature requiring instant data synchronization across clients.

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When the user wants to plan a product launch, feature announcement, or release strategy. Also use when the user mentions 'launch,' 'Product Hunt,' 'feature release,' 'announcement,' 'go-to-market,' 'beta launch,' 'early access,' 'waitlist,' 'product update,' 'how do I launch this,' 'launch checklist,' 'GTM plan,' or 'we're about to ship.' Use this whenever someone is preparing to release something publicly. For ongoing marketing after launch, see marketing-ideas.

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When the user wants to create or optimize in-app paywalls, upgrade screens, upsell modals, or feature gates. Also use when the user mentions "paywall," "upgrade screen," "upgrade modal," "upsell," "feature gate," "convert free to paid," "freemium conversion," "trial expiration screen," "limit reached screen," "plan upgrade prompt," "in-app pricing," "free users won't upgrade," "trial to paid conversion," or "how do I get users to pay." Use this for any in-product moment where you're asking users to upgrade. Distinct from public pricing pages (see page-cro) — this focuses on in-product upgrade moments where the user has already experienced value. For pricing decisions, see pricing-strategy.

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Build a "product description" repo for a software product — a set of prose documents describing, from the outside in, what the user sees, what they can do, and exactly what happens when they do it, written from the code and tests, then verified against the running product and triaged into a bug list. Works for any product with a user (canvas editors, web apps, CLIs, chat products, mobile apps). Use when the user asks to "write a product description for X", "describe the user experience of X", "document how X behaves for the user", "make a behavior-spec repo", or wants a feature-by-feature, event-by-event account of an app's behavior rather than API docs. Also use to resume or extend an existing product description repo.

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