「stream」の検索結果

Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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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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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

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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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Java coding standards for Spring Boot services: naming, immutability, Optional usage, streams, exceptions, generics, and project layout.

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Integrate Convex static self hosting into existing apps using the latest upstream instructions from get-convex/self-hosting every time. Use when setting up upload APIs, HTTP routes, deployment scripts, migration from external hosting, or troubleshooting static deploy issues across React, Vite, Next.js, and other frontends.

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Azure Event Hubs SDK for Rust. Use for sending and receiving events, streaming data ingestion.

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High-throughput event streaming and real-time data ingestion.

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Azure Event Hubs SDK for Python streaming. Use for high-throughput event ingestion, producers, consumers, and checkpointing.

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Rebuild the vault dependency graph (_graph.md) via the deterministic generator script. $graph forces a full rebuild; $graph last (run after every $sync) rebuilds only if the vault changed; $graph [N] is treated as last. The generator reads the vault and writes _graph.md directly, so the file never streams through a model response.

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Rebuild the vault dependency graph (_graph.md) via the deterministic generator script. /graph forces a full rebuild; /graph last (run after every /sync) rebuilds only if the vault changed; /graph [N] is treated as last. The generator reads the vault and writes _graph.md directly, so the file never streams through a model response.

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Configuração e diagnóstico de Nginx — reverse proxy, TLS, HTTP/2, HTTP/3, cache, compressão, rate limit e load balancing. Use quando o usuário disser "nginx", "reverse proxy", "502", "504", "certificado", "SSL", "TLS", "rate limit", "cache", "upstream".

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Add a standard AdwAboutDialog wired to app metadata, plus the AppStream metainfo file it should share data with. Use when adding an About entry, release notes, credits, or preparing app metadata.

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Build modern Next.js 13+ applications using App Router architecture with Server Components, Client Components, and advanced routing patterns. Use when implementing server-first rendering, creating nested layouts, building parallel routes, implementing intercepting routes, using React Server Components, optimizing data fetching with server-side async components, implementing streaming with Suspense, managing client-side interactivity boundaries, or leveraging Next.js 13+ app directory features for performant, SEO-friendly React applications.

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Build efficient React applications using Next.js Server Components that render on the server, reducing client bundle size, improving performance, and enabling direct database access. Use when fetching data server-side, reducing JavaScript bundle size, accessing databases directly in components, implementing streaming with Suspense, creating layouts that only render once, optimizing Core Web Vitals, or building SEO-friendly applications with server-first architecture.

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Refresh drift-prone documentation against current code. Reads docs/architecture/freshness-catalog.yml, diffs against the last sweep's upstream/main anchor, regenerates mechanical entries, processes editorial markers, and opens one PR per sweep with a report file.

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Build generative UI apps with OpenUI and OpenUI Lang — the token-efficient open standard for LLM-generated interfaces. Use when mentioning OpenUI, @openuidev, generative UI, streaming UI from LLMs, component libraries for AI, or replacing json-render/A2UI. Covers scaffolding, defineComponent, system prompts, the Renderer, and debugging OpenUI Lang output.

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