bio-rna-quantification-count-matrix-qc
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.
npx skills add BioTender-max/awesome-bio-agent-skills --skill count-matrix-qc --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.
## Version Compatibility Reference examples tested with: DESeq2 1.42+, ggplot2 3.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+, scipy 1.12+, seaborn 0.13+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Count Matrix QC **"Check my count matrix for outliers and batch effects"** → Perform PCA, sample-sample correlation, library size assessment, and outlier detection before running differential expression. - R: `DESeq2::vst()` → `plotPCA()`, sample distance heatmap - Python: `sklearn.decomposition.PCA`, `seaborn.clustermap` Quality control and exploratory analysis of count matrices before differential expression. ## Load and Inspect Counts **Goal:** Assess count matrix quality before differential expression by detecting outliers, batch effects, and sample relationship problems. **Approach:** Load counts into DE
- Version Compatibility
- Load and Inspect Counts
- R
- Python
- Basic Statistics
- Filter Low-Count Genes
- Normalize for Visualization
- R (DESeq2 VST)
- Python (log2 CPM)
- Sample Correlation
- PCA Analysis
- Detect Outliers
- Check for Batch Effects
- Library Complexity
What does the bio-rna-quantification-count-matrix-qc skill do?
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill count-matrix-qc --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.