Data & ReproStatistics & Data AnalysisFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-metabolomics-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

LC-MS/GC-MS: preprocessing → annotation → statistical analysis.

OpenClawNanoClawAnalysisReproductionbio-workflows-metabolomics-pipeline🧠 bioos extended suitebioos extended bioinformatics suitelc

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

mzml_files <- list.files('data/', pattern = '\\.mzML$', full.names = TRUE) sample_data <- read.csv('sample_metadata.csv').
raw_data <- readMSData(mzml_files, mode = 'onDisk').
pData(raw_data) <- sample_data.
cat('Loaded', length(mzml_files), 'samples\n').

Source Doc

Excerpt From SKILL.md

Complete R Workflow

library(xcms)
library(MSnbase)
library(MetaboAnalystR)
library(ggplot2)

## === 2. PEAK DETECTION ===

cwp <- CentWaveParam(
    peakwidth = c(5, 30),
    ppm = 25,
    snthresh = 10,
    prefilter = c(3, 1000),
    mzdiff = 0.01,
    noise = 1000
)

xdata <- findChromPeaks(raw_data, param = cwp)
cat('Detected', nrow(chromPeaks(xdata)), 'peaks\n')

## === 3. RETENTION TIME ALIGNMENT ===

xdata <- adjustRtime(xdata, param = ObiwarpParam(binSize = 0.6))
cat('Aligned retention times\n')

Use cases

Use bio-workflows-metabolomics-pipeline for statistical testing and quantitative analysis.
Apply bio-workflows-metabolomics-pipeline to research datasets that require rigorous inference.