'downstream' 검색 결과

Prepare single-cell or single-nucleus RNA-seq analysis by checking inputs and selecting workflows that turn FASTQ sequencing files into count matrices. Route quality checks, cell annotation, clustering, and UMAP visualization to the embedded downstream skill.

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• Start single-cell RNA-seq analysis from FASTQ files
• Choose a workflow for generating count matrices
• Route existing matrices to quality checks and cell annotation

Plan or run bulk RNA-seq processing from sequencing reads to count matrices, tables of expression counts across samples. Check sample metadata, reference consistency, read mapping, and quantification quality, and produce summaries for downstream analysis.

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• Generate count matrices from FASTQ files
• Check reference files and sample metadata
• Review mapping and quantification quality

Validate FASTQ sequencing files, run local quality checks, and interpret reports to decide whether trimming is needed. Optionally remove adapters or low-quality read ends while preserving original reads and their quality reports.

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• Check sequencing quality before downstream analysis
• Summarize quality reports across multiple samples
• Assess whether adapter or quality trimming is needed

Prioritizes candidate genes from GWAS, studies linking genetic variants to traits. Combines locus predictions, gene expression evidence, and rare variant support into ranked results with source attribution, confidence labels, reproducible files, and optional figures.

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• Find candidate genes for a disease or trait
• Rank genes near specified lead variants
• Compare evidence and tissue support across genes

Gather business context before analysis by checking connected or provided sources for metric definitions, recent changes, and decision background. Produce a focused context note that preserves source references, conflicting evidence, assumptions, and remaining gaps.

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• Clarifying metric definitions before analysis
• Checking recent changes before investigating performance
• Reconciling conflicting sources before writing a report

Assess whether data is trustworthy enough for analysis, dashboards, experiments, or modeling. Check missing values, duplicates, consistency, freshness, and changes over time, then explain the evidence, downstream risks, likely causes, and practical fixes.

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• Check missing values and duplicate records
• Investigate sudden changes in data quality
• Reconcile conflicting sources and metric definitions

Write and troubleshoot native Python in n8n Code nodes. Covers data filtering and transformation, migration from older Python code, valid return formats, and restricted execution environments, including cases where errors pass unprocessed input downstream.

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• Filtering and aggregating data in Python Code nodes
• Migrating legacy Python (Beta) code
• Fixing input-variable and return-format errors

Convert protein sequences into numerical features with Meta AI's ESM-2 for machine learning. Extract features for individual amino acids or whole sequences, score mutations, and predict which positions in a protein may contact each other.

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• Extracting protein features for machine learning
• Scoring the effects of amino acid mutations
• Predicting contacts from protein sequences

Use Evo 2 to score DNA sequences, turn genomic regions into numerical representations for classification, and generate sequences from a supplied prefix. Compare reference and variant sequences or assess coding and regulatory regions across species.

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• Comparing scores before and after a DNA variant
• Preparing numerical features for genomic region classification
• Generating DNA from a supplied prefix

Inspect scientific data files to understand their format, structure, and quality. Covering over 200 formats, this skill produces Markdown reports with statistical summaries, potential issues, and recommendations for preprocessing, visualization, and further analysis.

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• Inspecting an unfamiliar scientific data file
• Checking missing values and duplicates in experimental tables
• Reviewing sequence lengths and quality scores in FASTQ files

Audit causal inference in a sewage and house prices study by comparing manuscript claims with R code. Review design assumptions, statistical uncertainty, and robustness, then produce a prioritized report with concrete fixes.

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• Comparing manuscript methods with R analysis code
• Auditing assumptions behind causal inference
• Checking standard errors and multiple testing

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

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求是方法论的入口与总原则。在每次新的顶层会话开始时加载一次，用「实事求是」约束全部判断，并只在明确适用时把任务路由到对应的方法论 skill；被派遣执行单一具体任务的子 agent 直接跳过。 English: Entry point and governing principle of the Qiushi methodology. Load once at the start of a top-level session to enforce "seek truth from facts" and route to a downstream skill only when it clearly helps. Delegated sub-agents on narrow tasks should skip it.

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Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

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Comprehensive markdown and Mermaid diagram writing skill that establishes text-based diagrams as the DEFAULT documentation standard. Use this skill when creating ANY scientific document, report, analysis, or visualization — it ensures all outputs are in version-controlled, token-efficient markdown with embedded Mermaid diagrams as the source of truth, with clear pathways to downstream Python or AI-generated images. Includes full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates ready to use.

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Validate coding-sequence CSVs, extract public CodonFM/Encodon embeddings, and choose checkpoints for downstream property modeling.

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Entry skill for Jetson / IGX BSP customization. Asks one core click-to-select setup questionnaire and passes prefilled answers to downstream setup skills.

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doca_telemetry_utils command line on a host with DOCA: discover the diagnostic-counter schema, translate counter names to binary Data IDs and back, and check per-device counter support before committing a DOCA Telemetry exporter config. Start here when telemetry counters vanish between the exporter and the collector: "my exporter ships but the collector sees nothing", "this metric silently drops downstream", "which counters does this BlueField expose", "translate this 0x... back to a counter name", "what do node / pcie_index / depth mean here", or "is this counter supported on this device", even without naming the tool. Writing exporter or collector code belongs to doca-telemetry-exporter / doca-telemetry; DTS deployment to doca-dts; DOCA install or repair to doca-setup.

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Use this skill to deploy and operate a CollectX (clx) based DOCA telemetry collector on a host or BlueField — wiring providers / counters into the collector, running the collection daemon, and shaping its exporters (Prometheus pull, Fluent Bit push, NetFlow, file / IPC) so the metrics actually leave the box. Trigger even when the user never says CollectX or clx — implicit phrasings: {collector emits nothing downstream}, {add a provider to the clx collector}, {turn on the Prometheus endpoint}, {ship counters to Fluent Bit from the DPU}, {daemon starts but no schema rows appear}. This skill owns the CollectX collection mechanism plus the operator's own doca-telemetry / doca-telemetry-exporter usage; it ROUTES the productized DOCA Telemetry Service (DTS) to public docs (AGENTS.md Non-goal #7), the reader API to doca-telemetry, and the publisher API to doca-telemetry-exporter. Refuse to invent clx symbols, provider names, schema fields, flags, or config paths — describe the class and route to the live source.

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Produce a token-bounded, citation-ready context slice from an existing Obsidian vault for a downstream agent or task. Use for "/wiki-context-pack", "use my vault as context", "context slice for X", "pack the wiki for my agent", or "bounded context for Y".

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[omh] Gathering candidate papers, datasets, or repos: source candidate inventory - prepare typed source candidates and acquisition status before downstream work; use ulw-research to fetch and cite them, or research-brief to turn them into a decision-ready brief. Use when the user says: source-finder, source finder, source acquisition, source intake, find papers and datasets, find datasets and repos, find papers, find arxiv link.

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[omh] Data pipeline work -- an ETL or streaming job, a backfill or replay, duplicate events, a schema change downstream, a lineage question, a data-quality regression: make every rerun idempotent, bound every replay, and gate each load on observed checks. Use when the user says: data-pipelines, data pipeline, data pipelines, etl, elt, etl pipeline, etl job, etl backfill.

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Apply before writing logic: choosing core types and data structures, sequencing scaffold-vs-feature work, asking what concurrent actors share. Get the data structures right so downstream code becomes obvious.

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Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analysis. Covers sample metrics, missing value patterns, replicate correlation, batch effects, and intensity distributions.

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