数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-workflows-microbiome-pipeline

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

Microbiome: 16S/ITS amplicon or shotgun → diversity → differential.

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

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

path <- 'raw_reads' silva_train <- 'silva_nr99_v138.1_train_set.fa.gz' silva_species <- 'silva_species_assignment_v138.1.fa.gz' metadata_file <- 'sample_metadata.csv。
fnFs <- sort(list.files(path，pattern = '_R1_001.fastq.gz'，full.names = TRUE)) fnRs <- sort(list.files(path，pattern = '_R2_001.fastq.gz'，full.names = TRUE)) sample_names <- sapply(strsplit(basename(fnFs)，'_')，[，1)。

原始文档

SKILL.md 摘录

Complete R Workflow

library(dada2)
library(phyloseq)
library(ALDEx2)
library(vegan)
library(ggplot2)

## Setup filtered files

filtFs <- file.path('filtered', paste0(sample_names, '_F_filt.fastq.gz'))
filtRs <- file.path('filtered', paste0(sample_names, '_R_filt.fastq.gz'))

## === 2. FILTER & TRIM ===

out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs,
                     truncLen = c(240, 160), maxN = 0, maxEE = c(2, 2),
                     truncQ = 2, rm.phix = TRUE, compress = TRUE, multithread = TRUE)

适用场景

Use bio-workflows-microbiome-pipeline ，用于 genomics 、 bioinformatics workflows。
Apply bio-workflows-microbiome-pipeline to sequencing，variant，或 omics analysis tasks。