bio-expression-matrix-metadata-joins
Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.
npx skills add BioTender-max/awesome-bio-agent-skills --skill metadata-joins --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: pandas 2.2+ 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. # Metadata Joins ## Load Sample Metadata **Goal:** Read sample metadata into a DataFrame aligned with the count matrix columns. **Approach:** Load metadata CSV with sample IDs as the index, matching count matrix column names. ```python import pandas as pd # Load metadata metadata = pd.read_csv('sample_info.csv', index_col=0) # Metadata should have samples as rows, attributes as columns # Index should match count matrix column names ``` ## Basic Join **Goal:** Align count matrix columns with metadata rows so samples are in matching order. **Approach:** Find common samples between both data sources, subset and reorder to ensure alignment. **"Match my sample metadata to my count matrix"** → Intersect sample identifiers between the
- Version Compatibility
- Load Sample Metadata
- Basic Join
- Handle Sample Name Mismatches
- Flexible Sample Name Matching
- Add Gene Annotations
- R: Create DESeq2 Data
- R: Create edgeR DGEList
- Create AnnData with Metadata
- Validate Metadata
- Sample Swap Detection
- Sex Check
- Experimental Design Guidance
- Reference Level Selection
What does the bio-expression-matrix-metadata-joins skill do?
Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill metadata-joins --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.