bio-expression-matrix-counts-ingest
Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantification results for downstream analysis.
npx skills add BioTender-max/awesome-bio-agent-skills --skill counts-ingest --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+, tximport 1.30+, tximeta 1.20+ 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 Ingestion ## Expression Units Decision Table | Unit | Source | Use for DE | Use for visualization | Cross-sample comparison | |------|--------|------------|----------------------|------------------------| | Raw counts | featureCounts, HTSeq, STAR | Yes (DE tools normalize internally) | No | No | | Estimated counts | Salmon, kallisto (via tximport) | Yes (with offset correction) | No | No | | TPM | Salmon, kallisto | No | Within-sample gene comparison | Partially (same composition caveat) | | FPKM/RPKM | Cufflinks, legacy tools | No | Within-sample only | No (composition bias) | | Normalized counts | DESeq2, edgeR | Via DE tool | Prefer VST/rlog | Yes | For differential expression, a
- Version Compatibility
- Expression Units Decision Table
- Transcript-Level vs Gene-Level Quantification
- Basic CSV/TSV Loading
- featureCounts Output
- Salmon Quant Files
- STAR ReadsPerGene Files
- HTSeq Count Files
- kallisto Abundance Files
- 10X Genomics Sparse Matrix
- AnnData H5AD Files
- RDS Files (from R)
- Combine Multiple Files
- Filter Low-Count Genes
What does the bio-expression-matrix-counts-ingest skill do?
Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantification results for downstream analysis.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill counts-ingest --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.