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bio-rna-quantification-tximport-workflow
Maintainer FreedomIntelligence · Last updated April 1, 2026
Import Salmon/Kallisto quantification into R/DESeq2 with tximport.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-rna-quantification-tximport-workflow
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Import transcript-level estimates from Salmon, kallisto, or other quantifiers into R for gene-level differential expression analysis.
- files <- c( sample1 = 'sample1_quant/quant.sf', sample2 = 'sample2_quant/quant.sf', sample3 = 'sample3_quant/quant.sf' ).
Source Doc
Excerpt From SKILL.md
Load transcript-to-gene mapping
tx2gene <- read.csv('tx2gene.csv') # columns: TXNAME, GENEID
Import at gene level
txi <- tximport(files, type = 'salmon', tx2gene = tx2gene)
## Summarize transcripts to gene level
txi <- tximport(files, type = 'salmon', tx2gene = tx2gene)
Use cases
- Use bio-rna-quantification-tximport-workflow for genomics and bioinformatics workflows.
- Apply bio-rna-quantification-tximport-workflow to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- rna-quantification/alignment-free-quant - Upstream Salmon/kallisto
- differential-expression/deseq2-basics - DESeq2 analysis
- differential-expression/edger-basics - edgeR analysis
- genome-intervals/gtf-gff-handling - GTF annotation parsing
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