SCI Skills

CN Directory
数据与复现蛋白质组与代谢组FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
BI

bio-workflows-proteomics-pipeline

维护者 FreedomIntelligence · 最近更新 2026年4月1日

DDA/DIA proteomics: search → quantification → differential abundance.

OpenClawNanoClaw分析处理复现实验bio-workflows-proteomics-pipeline🧠 bioos extended suitebioos extended bioinformatics suitedda

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-proteomics-pipeline

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

2 min

核心说明

  • proteins <- read.delim('proteinGroups.txt'，stringsAsFactors = FALSE) cat('Loaded'，nrow(proteins)，'protein groups\n')。
  • proteins <- proteins[proteins$Potential.contaminant!= '+' & proteins$Reverse!= '+' & proteins$Only.identified.by.site!= '+'，] cat('After filtering：'，nrow(proteins)，'proteins\n')。

原始文档

SKILL.md 摘录

Complete R Workflow

library(limma)
library(ggplot2)
library(pheatmap)

## Extract LFQ intensities

lfq_cols <- grep('^LFQ\\.intensity\\.', colnames(proteins), value = TRUE)
intensities <- proteins[, lfq_cols]
rownames(intensities) <- proteins$Majority.protein.IDs
colnames(intensities) <- gsub('LFQ\\.intensity\\.', '', colnames(intensities))

## === 2. LOG2 TRANSFORM & NORMALIZE ===

intensities[intensities == 0] <- NA
log2_int <- log2(intensities)

适用场景

  • Use bio-workflows-proteomics-pipeline in 科研工作流 aligned ，支持 this subject area。
  • Follow upstream documentation ，用于 full working procedure。

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

  • proteomics/data-import - Load MS data formats
  • proteomics/proteomics-qc - Quality control before analysis
  • proteomics/quantification - Normalization methods
  • proteomics/differential-abundance - Statistical testing details
  • proteomics/ptm-analysis - Phosphoproteomics and other PTMs
  • data-visualization/specialized-omics-plots - Volcano plots

相关技能

相关技能

返回目录
BI
数据与复现蛋白质组与代谢组

bio-metabolomics-lipidomics

Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipid…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
数据与复现蛋白质组与代谢组

bio-metabolomics-metabolite-annotation

Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
数据与复现蛋白质组与代谢组

bio-metabolomics-msdial-preprocessing

MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and expor…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
数据与复现蛋白质组与代谢组

bio-metabolomics-pathway-mapping

Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology…

OpenClawNanoClaw分析处理
FreedomIntelligence/OpenClaw-Medical-Skills查看