omics-analysis-guide
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
npx skills add BioTender-max/awesome-bio-agent-skills --skill omics-analysis-guide --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Describes a three-tiered approach to omics data analysis (transcriptomics, proteomics), prioritizing validated pipelines, then standard workflows, and finally custom methods. It includes guidance on when to use each tier, how to cite tools, and example workflows for RNA-seq and proteomics, plus a decision framework and quality-control guidance.
How it works
Outlines a procedural hierarchy:
- Option 1: Search for validated analysis methods (Method 1: literature search; Method 2: review standard workflows). If validated pipelines exist, document pipeline name, version, reference, validation, and parameters.
- If none found, proceed to Option 2: Use Standard Analysis Workflows, detailing QC steps, missing-value handling, normalization, statistical test selection, multiple testing correction, and visualization.
- Provides step-by-step preprocessing and analysis guidance, including imputation rules (MNAR uses minprob; MCAR/MAR uses KNN), normalization methods, test assumptions checks (normality, variance, sample size), and BH-FDR for p-value correction.
- Includes Decision Framework and a data-type/experiment-oriented decision table with recommended tiers and specific approaches.
- Mentions essential artifacts to document (steps, parameters, results) and visualization outputs (volcano plot, PCA).
When to use it
Use when planning omics data analyses (transcriptomics and proteomics) to decide between validated pipelines (Option 1), standard workflows (Option 2), or custom analyses (Option 3) based on data type, available pipelines, and dataset characteristics.
What it can touch
Details the workflow steps and tools conceptually but does not enumerate executable tool commands beyond general references (e.g., DESeq2, edgeR, MaxQuant, SHapiro-Wilk, Levene, Benjamini-Hochberg). It names and describes tools and methods but does not provide a single runnable script in this summary.
Caveats
Includes license notes (CC BY 4.0) and notes commercial use can be allowed; emphasizes reliance on validated pipelines first and cautions about limitations of standard workflows when validated pipelines are available.
# Omics Data Analysis Guide: Three-Tiered Approach --- ## Metadata **Short Description**: Comprehensive guide for analyzing omics data (transcriptomics, proteomics) using validated pipelines, standard workflows, or custom analysis methods. **Authors**: HITS **Version**: 1.0 **Last Updated**: December 2025 **License**: CC BY 4.0 **Commercial Use**: Allowed ## Citations and Acknowledgments ### If you use validated pipelines or tools (Option 1): - **Citation**: Always cite the original publication associated with each tool or pipeline - **Acknowledgment**: Cite the specific tools and methods used in your analysis ### If you use standard workflows (Option 2): - **Acknowledgment Statement**: "Analysis performed using standard omics data analysis workflows and best practices" - **Citation for RNA-seq analysis**: Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. PMID: 23104886 - **Citation for proteomics**: Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26(12):1367-72. PMID: 19029910 --- ## Overview This guide provides a
- Metadata
- Citations and Acknowledgments
- If you use validated pipelines or tools (Option 1):
- If you use standard workflows (Option 2):
- Overview
- Key Concepts
- Validated Pipeline vs. Standard Workflow vs. Custom Analysis
- Missing Value Mechanisms (MCAR / MAR / MNAR)
- Test Assumptions and Test Selection
- Multiple Testing Correction
- Decision Framework
- Decision Table
- Option 1: Search for Validated Analysis Methods (Recommended First)
- 1.1 Search for Validated Analysis Pipelines
What does the omics-analysis-guide skill do?
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill omics-analysis-guide --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.