microbiome-workflow 开源项目推荐（28 个）

grimmlab /MicrobiomeBestPracticeReview

使用扩增子和宏基因组测序进行微生物组分析的当前挑战与最佳实践方案。

cafferychen777 /MicrobiomeStat

追踪、分析、可视化：用MicrobiomeStat揭开你的微生物组的时间模式

anwarMZ /CoMW

Comparative Metatranscriptomics Workflow

HPCBio /dada2-rs

DADA2, reimplemented in Rust

cafferychen777 /MicrobiomeStat-Turtorial-Professional-Version

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

biocorecrg /microbiome_procedures

Mothur procedures for 16S and ITS analysis

linsalrob /atavide_lite

A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings are specific for our compute resources. Read the docs at:

TomC-93 /Tree-Root-Microbiome-Project

The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.

Brochado-Kith /microbiome_analysis

The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.

natmurad /amplicon16S

Analysis for amplicon data

DOieGYuan /gone

Use one command to perform genome-centric metagenomics using state-of-the-art methods

cafferychen777 /MicrobiomeStat-Shiny

A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.

EdwinMosesAppiah /Gastric-Microbiome-and-Gastric-Carcinogenesis

This repository contains all codes used in the "The Gastric Microbiome and Gastric Carcinogenesis: Bacterial Diversity, Co-occurrence Patterns and Predictive Models" projects

ahmedmoustafa /ALS

Analysis of the gut microbiome of Amyotrophic Lateral Sclerosis (ALS) patients using the DADA2 workflow

jjcolgan /Bodke-Script

Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2

hermidalc /dragonfish

A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG

glickmac /Microbiome_Demo

A repository containing a demo microbiome workflow for R and Python

mdelacuba /script-repo-microbiome-2025

Script repository related to the data processing and analyses of the study: "Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes".

Azurdix /MicrobiomeAnalysis

This repository is a place for codes I have used during my PhD for microbiome analysis of spider egg sacs. Two species were analysed: Parasteatoda tepidariorum and Pardosa lugubris. Three egg sac's conditions: environment + silk + eggs. This code was created in this 'simple adaptation' vibes, so I can tweak it here and there for the future studies.

Azurdix /MicrobiomeHeatMap

This was created and refined during my PhD as the part of the scientific project. Codes are highly customizable. Watch out - Each code does a heatmap for absolutely different thing.