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bio-rna-quantification-tximport-workflow
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Import Salmon/Kallisto quantification into R/DESeq2 with tximport.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-rna-quantification-tximport-workflow
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Import transcript-level estimates ，面向 Salmon，kallisto，或 other quantifiers into R ，用于 gene-level differential expression analysis。
- files <- c( sample1 = 'sample1_quant/quant.sf'，sample2 = 'sample2_quant/quant.sf'，sample3 = 'sample3_quant/quant.sf' )。
原始文档
SKILL.md 摘录
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)
适用场景
- Use bio-rna-quantification-tximport-workflow ，用于 genomics 、 bioinformatics workflows。
- Apply bio-rna-quantification-tximport-workflow to sequencing，variant，或 omics analysis tasks。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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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