bio-rna-quantification-tximport-workflow
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tximport-workflow --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+, Salmon 1.10+, edgeR 4.0+, kallisto 0.50+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - 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. # tximport Workflow **"Import Salmon/kallisto results into DESeq2"** → Summarize transcript-level abundance estimates to gene-level counts with proper length-offset correction for use in DESeq2 or edgeR. - R: `tximport::tximport(files, type='salmon', tx2gene=tx2gene)` Import transcript-level estimates from Salmon, kallisto, or other quantifiers into R for gene-level differential expression analysis. ## Basic tximport **Goal:** Import transcript-level quantifications from Salmon or kallisto into R as gene-level counts with proper length-offset correction for DESeq2 or edgeR. **Approach:** Create a transcript-to-gene mapping from a GTF or biomaRt, then run tximport on the quantification files to produce a gene-level count matrix with length-scaled TPM
- Version Compatibility
- Basic tximport
- Creating tx2gene Mapping
- From GTF (using GenomicFeatures)
- From Ensembl (using biomaRt)
- From Salmon quant.sf
- Import Types
- Gene-Level Summarization (Default)
- Transcript-Level (No Summarization)
- Scaled TPM (for visualization)
- Source-Specific Import
- Salmon
- kallisto
- RSEM
What does the bio-rna-quantification-tximport-workflow skill do?
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tximport-workflow --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.