「scd」の検索結果

We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positi

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Star schema, snowflake schema, SCD types, and Kimball methodology for analytical data modeling. Activate on: dimensional model, star schema, snowflake schema, SCD, fact table, dimension table, Kimball, grain, surrogate key. NOT for: dbt implementation (use dbt-analytics-engineer), warehouse tuning (use data-warehouse-optimizer).

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。

Star schema, snowflake schema, SCD types, and Kimball methodology for analytical data modeling. Activate on: dimensional model, star schema, snowflake schema, SCD, fact table, dimension table, Kimball, grain, surrogate key. NOT for: dbt implementation (use dbt-analytics-engineer), warehouse tuning (use data-warehouse-optimizer).

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The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly fou

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Work with SuperCollider projects as files - the shape of a .scd piece, how to read and write one with sc_project, how to send the file that is on disk into the live session with sc_load, what state belongs in the session and what belongs in the file, and how to package a piece the SuperCollider way (a folder with its .scd, its SynthDefs, and a Quark-style layout) instead of inventing a format.

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Facilitate Kimball-style dimensional (data warehouse / BI) modeling sessions through conversation, producing DimML (Dimensional Modeling Language, YAML) as the primary artifact plus a bus-matrix + star-schema HTML. Use whenever the user wants to design fact tables, dimensions, a star schema, or a bus matrix — declaring grain, choosing SCD types, identifying conformed dimensions and measures (additivity) — by grilling one step at a time. Also invoke for refining an existing DimML, or when the user says "ディメンショナル・モデリング", "ディメンションモデリング", "スタースキーマ", "バスマトリクス", "ファクト表を設計したい", "グレインを決めたい", "DimML を育てたい", "Kimball で整理したい".

Process, quality-control, annotate, and visualize single-cell or single-nucleus RNA-seq datasets across tissues and species. Use when Codex needs to build, adapt, or review a general scRNA-seq QC pipeline; choose dataset-appropriate cell-level filters from QC distributions; run required scDblFinder-based doublet and ambient-RNA filtering; annotate cells with matched references or marker-based fallbacks; or generate global and per-group UMAP visualizations for large scRNA-seq datasets.

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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

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Query journal indexing/inclusion status on CNKI - check which databases include a journal (北大核心, CSSCI, CSCD, SCI, EI, etc.), get impact factors and evaluation data. Use when user asks about a journal's level, indexing, or ranking.

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Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.

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Think and work like an expert Data Engineer. Use when a task calls for Data Engineer judgment. Reasons from idempotent ELT, medallion bronze/silver/gold, Kimball grain and SCD2, CDC/Debezium and watermark incremental loads, dbt/GX quality gates, Airflow/Dagster orchestration, Iceberg/Delta lakehouse MERGE, data contracts and freshness SLIs while treating silent join drops, duplicate amplification, schema drift, and green-DAG-wrong-numbers as first-class failure modes.

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数据工程 — 数据平台从业者的认知操作系统, 覆盖把数据从源系统搬运成可靠 / 可查询 / 可信赖形态供分析 / ML / 数据产品消费的全生命周期 (生成 → 摄取 → 存储 → 转换 → 服务 + 安全/数据管理/DataOps/数据架构/编排/软件工程 六条暗流, Reis & Housley 框架): 摄取与集成 (批 + CDC 变更数据捕获 Debezium + EL 工具 Fivetran/Airbyte/Meltano/dlt + Kafka Connect + schema drift) / 存储与文件表格式 (对象存储数据湖 + 列存 Parquet/ORC/Arrow/Avro + 开放表格式 Apache Iceberg/Delta Lake/Apache Hudi + lakehouse + 分区/compaction) / 转换与建模 (ELT dbt/SQLMesh + Spark + 维度建模 Kimball + Inmon + Data Vault + 大宽表 OBT + 渐变维 SCD + 增量模型 + 语义/指标层) / 编排与工作流 (Apache Airflow/Dagster/Prefect/Mage/Kestra/Apache DolphinScheduler + DAG + 幂等 + 回填 backfill + 数据资产调度) / 批流与实时 (Apache Kafka/Apache Flink/Spark Structured Streaming/Kinesis/Pulsar/Redpanda + Lambda vs Kappa + watermark/窗口/exactly-once + 流式 SQL Materialize/RisingWave + 实时 OLAP ClickHouse/Apache Druid/Apache Pinot/StarRocks/Apache Doris) / 数仓与查询引擎 (Snowflake/BigQuery/Redshift/Databricks SQL/Trino/Presto/DuckDB/Polars + 存算分离 + MPP) / 数据质量测试与可观测性 (dbt tests/Great Expectations/Soda + 数据契约 + Monte Carlo data downtime + 新鲜度/量/schema 异常检测) / 数据治理编目与血缘 (DataHub/Amundsen/OpenMetadata/Unity Catalog + 列级血缘 + PII 分类 + 访问控制 + GDPR) / DataOps 与可靠性 (数据 CI/CD + 转换版本控制 + 环境隔离 + 幂等重处理 + 数据 SLA/SLO + 计算存储 FinOps) / 数据架构范式 (现代数据栈 + lakehouse + data mesh + data fabric + 去中心化 vs 中心化所有权) / 分析工程角色 (dbt 时代连接数据工程与分析的桥) — 不含 数据科学/ML 建模本身 (是下游消费者) / BI 仪表盘制作 (serving 下游) / 数据分析报表为终点 / 'data engineer = 跑 Hadoop 的' 过时窄化 / 通用后端应用开发 (平行学科) (Data Engineering — the cognitive operating system of practitioners who design, build, and operate the data platform: moving data from source systems into reliable, queryable, trustworthy form for analytics / ML / products, covering (a) the data engineering lifecycle (generation → ingestion → storage → transformation → serving, with the undercurrents security / data management / DataOps / data architecture / orchestration / software engineering — Reis & Housley framing), (b) ingestion & integration (batch + CDC change-data-capture with Debezium, EL tools Fivetran / Airbyte / Meltano / dlt, Kafka Connect, API + file + database sources, schema drift handling), (c) storage & file/table formats (object storage data lakes, columnar formats Parquet / ORC / Arrow / Avro, open table formats Apache Iceberg / Delta Lake / Apache Hudi, lakehouse architecture, partitioning / compaction / Z-ordering), (d) transformation & modeling (ELT with dbt / SQLMesh, Spark, dimensional modeling Kimball, Inmon CIF, Data Vault, One Big Table / wide tables, normalization vs denormalization, slowly changing dimensions, incremental models, the semantic / metrics layer), (e) orchestration & workflow (Apache Airflow, Dagster, Prefect, Mage, Kestra, Apache DolphinScheduler, DAGs, idempotency, backfills, data-aware / asset-based scheduling), (f) batch vs streaming & real-time (Apache Kafka, Apache Flink, Spark Structured Streaming, Kinesis / Pulsar / Redpanda, the Lambda vs Kappa debate, watermarks / windowing / exactly-once, streaming SQL Materialize / RisingWave, real-time OLAP ClickHouse / Apache Druid / Apache Pinot / StarRocks / Apache Doris), (g) warehouses & query engines (Snowflake, BigQuery, Redshift, Databricks SQL, Trino / Presto, DuckDB, Polars, decoupled storage & compute, MPP), (h) data quality, testing & observability (dbt tests, Great Expectations, Soda, data contracts, Monte Carlo / data downtime, freshness / volume / schema anomaly detection, unit / integration testing of pipelines), (i) data governance, catalog & lineage (DataHub, Amundsen, OpenMetadata, Unity Catalog, column-level lineage, PII / data classification, access control, GDPR / data privacy), (j) DataOps & reliability (CI/CD for data, version control of transformations, environments, idempotent reprocessing, SLAs / SLOs for data, cost / FinOps for compute & storage), (k) data architecture paradigms (modern data stack, data lakehouse, data mesh, data fabric, decentralized vs centralized ownership), (l) the analytics engineering role (the dbt-era bridge between data engineering and analysis); N

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Interviews a researcher in rounds until an idea, design, or draft has no unexamined decision — numbered questions, each with why it matters and a recommended answer, facts looked up rather than asked, and settled decisions written to a file. Stages are idea (topic or hunch to a falsifiable question and contribution claim), design (estimand, identification, sample and power, measurement, analysis plan, pre-registration, venue), and defend (reviewer objections to a finished design or draft). Use when the user says "grill me", asks to stress-test or poke holes in an idea, design, or plan, asks what they are assuming, or brings an idea that is not yet a design. --plan grills software or process plans.

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Turns raw captures (dictated braindumps in a deliverable's inbox/, or recent macwhspr dictation-log entries) into proposed planning-wiki changes, shown as one unified diff. Classifies each statement as a decision, evidence claim, question, task, or dropped item, traces it to its capture paragraph, tags unconfirmed names, numbers, and citations UNRESOLVED, and writes decisions only with the author's assent. Edits only the planning wiki, never source files. Use when asked to intake, absorb notes, or process the inbox, or after dictating notes from a talk, meeting, or reading session.

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Opens a deliverable (talk, course module, paper, book chapter, or referee report) for AI-assisted work across sessions. Interviews the author for the manifest, then scaffolds deliverable.yml, an append-only HANDOFF.md, a numbered planning/ wiki with open questions, an inbox/ for dictated braindumps, a gitignored checks/, and the house deck template for talks. Use when starting deadline-driven work that spans sessions, or when asked to open a deliverable, set up a talk, paper, or module for the pipeline, or make a manifest. Not for one-off tasks.

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Reviews a whole deliverable (talk, course module, paper, chapter, or referee report) against its manifest without rewriting it. Runs a deterministic gate for build, citations, numbers, facts, and leaks and stops on failure, then runs a finder over each section and a strong-model pass over the whole work, and adjudicates into checks/<date>/findings.json and report.md with anchored findings, severities, and honest NOT CHECKED coverage within a dollar budget. Use when asked to lint or review the whole talk, module, or paper, for a pre-ship review, or for the night shift. Revision stays serial and author-led.

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Start-of-session situational report for a research or code repository. Reads the handoff, log, or status files the project actually keeps, checks live git state, and reports the objective, verified baseline, open tasks, blockers, and next actions, flagging where the documents and the repository disagree. Use when resuming work after time away or before changing anything. Its end-of-session twin is finished.

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End-of-session closure for a research or code repository. Records what changed into the project's own handoff and log files, separating verified work from work merely attempted, and reports what is left uncommitted. Use when wrapping up a session so the next one can resume without re-deriving state. Its start-of-session twin is sitrep.

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Runs several language models as independent coders on one labeling or discovery task and treats disagreement as data. Covers diverse panel assembly, independent voting, consensus rules, Cohen’s and Fleiss kappa, Krippendorff’s alpha, correlated-error limits on validity claims, human validation, and reporting. Use when the user asks about a council, panel, ensemble, or jury of models, how to combine model labels, or what kappa or alpha to report for model coders. Single-model codebook and validation work goes to text-classification, per-item confidence to llm-calibration-logprobs.

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Runs several language models as independent coders on the same labeling or discovery task and reads their disagreement as data — panel assembly for model diversity, keeping votes independent, consensus rules, agreement statistics (Cohen's and Fleiss kappa, Krippendorff's alpha), the correlated-errors caveat that stops agreement being mistaken for validity, human validation beyond the panel, and reporting. Use when the user asks about a council, panel, ensemble, or jury of models, asks how to combine several models' labels, or asks what kappa or alpha to report for model coders. Single-model codebook and validation work goes to text-classification, per-item confidence to llm-calibration-logprobs.

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Spawns full Claude Code peer sessions in separate terminal panes and git worktrees, real sessions rather than subagents, each with a directed task and contract brief, monitored and merged by the spawning lead. Detects the environment and uses herdr first, then tmux, then a native claude background agent. Use when work must persist or run beside the current session, needs a separate worktree or permission settings, should remain user-steerable in a visible pane, or when the user asks to spawn, hand off, or parallelize full sessions. Also spawns Codex peers into those panes. Excludes bounded consults and subagent-scale work.

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House rules and craft for LaTeX Beamer slide decks (lectures, seminars, talks), drawn from the author's own Overleaf edits and published slide-design guidance. Covers storyboarding, frame titles, slide prose, word and frame budgets, layout without overfull boxes, XeLaTeX fonts and Korean (xeCJK), color, figures and screenshots, Overleaf source hygiene, speaker notes, and a build-and-QA loop with a contact sheet. Use when writing, editing, reviewing, or building a Beamer deck, theme, or storyboard. A course skill supplies course facts and the frame skeleton; this skill supplies the craft. Not for HTML or PowerPoint decks, posters, or papers.

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Spawn full peer Codex or Claude sessions in their own panes and git worktrees — real sessions, not subagents — briefed by the lead and merged back. Not for bounded consults a subagent covers. Use when work must outlive or run beside this session, needs its own worktree, or must stay user-steerable.

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Scaffolds or audits a social-science replication package and evaluates the manuscript and archived research objects against FAIR principles. Scaffold mode writes the folder structure, README, master.R, figure-table crosswalk, codebook, LICENSE placeholder, and .gitignore; audit mode grades the package against a pre-release checklist and audits data, code, materials, identifiers, licenses, access restrictions, and availability statements. Use when setting up or repairing a package, checking one before submission, auditing FAIR compliance, or drafting availability statements. Adapted from Yusaku Horiuchi’s replication-package-guide.

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