「oss」の検索結果

ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene. Use to annotate variants with regulatory tracks, find open chromatin in a cell type, or fetch peak files for ChIP/ATAC analysis. For regulatory variant scoring use regulomedb-database; for GWAS associations use gwas-database.

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Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.

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Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).

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Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use opentargets-database.

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ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.

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Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key). For clinical pathogenicity use clinvar-database; for population frequencies use gnomad-database.

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Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nomenclature or gene coordinates. Use for QTL support, cross-strain comparison, mouse model selection, and ontology-driven phenotype discovery. Use monarch-database for disease-gene-phenotype knowledge graphs; ensembl-database for mouse genome annotations.

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Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.

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Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble plots → cross-condition compare. Human, mouse. Use liana for pure-Python.

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Guide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organism codes, API failure handling with offline fallbacks, cross-condition comparisons, and answer-first reporting. Consult when running enrichment with clusterProfiler or gseapy.

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Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools. Covers PICO framework for clinical questions, three-tiered search (database-specific, AI-assisted, content extraction), PubMed field tags and MeSH, boolean query construction, and full-text extraction. Use when planning a literature search or choosing a search tier.

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Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.

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Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values. Covers why bulk matrix shortcuts fail, correct pairwise deletion, degenerate input filtering, and large-dataset performance. Use statistical-analysis for test choice; shap-model-explainability for interpretability.

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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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Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi-modal. Rigid/affine/deformable registration, threshold/region-growing segmentation, Gaussian/morph filtering, label stats, format conversion. Use to align volumes across timepoints/modalities, segment fluorescence, or convert DICOM→NIfTI.

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Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.

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DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed.

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Comprehensive best practices for robot perception systems covering cameras, LiDARs, depth sensors, IMUs, and multi-sensor setups. Use this skill when working with RGB image processing, depth maps, point clouds, sensor calibration (intrinsic, extrinsic, hand-eye), object detection, semantic segmentation, 3D reconstruction, visual servoing, or perception pipeline optimization. Trigger whenever the user mentions OpenCV, Open3D, PCL, RealSense, ZED, OAK-D, camera calibration, AprilTags, ArUco markers, stereo vision, RGBD, point cloud filtering, ICP registration, coordinate transforms, camera intrinsics, distortion correction, image undistortion, sensor streaming, frame synchronization, or any computer vision task in a robotics context. Also covers multi-camera rigs, time synchronization across sensors, perception latency budgets, and production deployment of perception pipelines.

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15-agent hierarchical mesh coordination for v3 implementation. Orchestrates parallel execution across security, core, and integration domains following 10 ADRs with 14-week timeline.

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Find and place the best 0DTE (zero-days-to-expiration) credit spreads from Interactive Brokers. Default execution route is the EMA9/EMA21 + VIX/VXN regime strategy (ema_vix_0dte.py), which auto-selects bull_put or bear_call from a bare EMA cross and skips the trade when the vol index is elevated (VXN ≥ 35 for NDX/QQQ, VIX ≥ 20 otherwise). Optional --rr-gate and --time-gate add red→red and bar-timing confirmation. Supports cash-settled indices (SPX, NDX, RUT, VIX) and any optionable stock/ETF. Manual spread type override is available via zero_dte.py. Requires TWS or IB Gateway running locally.

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Report delta-adjusted notional exposure across all IBKR accounts. Calculates option deltas using Black-Scholes and reports long/short exposure by account and underlying. Use when user asks about delta exposure, portfolio risk, or directional exposure.

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Generate a comprehensive portfolio action report with earnings dates and risk assessment. Use when user asks for portfolio review, action items, earnings risk, or position management across IB accounts. Requires TWS or IB Gateway running locally.

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Operational knowledge for the daily-brief digest pipeline (this project). RSS/API fetchers, pluggable LLM enrichment (default claude CLI on Max; also anthropic/openai/deepseek/minimax API), trading section, HTML rendering, cross-platform scheduler integration (Windows Task Scheduler / macOS launchd / Linux cron). Load when the user asks about running daily / regenerating sections / debugging a failed run / adding or disabling sources / LLM quota / scheduler / why a tab shows wrong data / why a source failed / switching LLM backend. Always prefer the documented npm commands over re-implementing logic. Diagnose by reading logs/daily-*.log first, then logs/llm-calls.jsonl for LLM-side issues.

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把一句话需求转成可复现、可验收视频工程的乔木智能剪辑导演。Use when the user asks to create, plan, edit, remix, explain, narrate, subtitle, animate, composite, or render a video—including one-line requests such as “制作一个科普视频：介绍 LLM 中的 RL”. Builds English-learning movie mixes, person profiles, explainers, code-drawn motion graphics (UI morph loops, showreels, kinetic-type promos, line-art/pixel/Three.js animation, lyric MVs), product launch videos, cinematic shorts, social clips, course/PPT videos, AI image/video/TTS/music-assisted stories, stock-footage stories, or multi-source montage. Routes across 33台词, ClipSeek/open media, local files, ListenHub, image generation, HTML/SVG/Canvas motion graphics with beat-grid storyboards and determinism probes, Manim, ffmpeg-full, captions, sound design, frame-0 video covers with YouTube thumbnails, and release checks.

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