💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Make Picrust2 Output Analysis and Visualization Easier

Scripts for reproducing results shown in Gupta VK et al. "A Predictive Index for Health Status using Species-level Gut Microbiome Profiling". Nature Communications, 2020. https://doi.org/10.1038/s41467-020-18476-8.

MicrobeRX

A computational tool for the prediction and identification of metabolites.

Data and analysis code for the Indian gut microbiota study

Gut microbiome study (from 2000 to 2020)

Deciphering microbial interactions with functional redundancy in human microbial community with partial information decomposition.

Les études de métagénomiques mettent en évidence la présence et l'absence de différentes souches dans un microbiome. Pour résumer les abondances, on peut établir des graphes de co-occurence via : Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data, Janko Tackmann, Joao Frederico …

🔬 Resources and notes on studying the human microbiome

Analysis and visualization of bioenergetic pathways in human gut microbiome datasets.

An Android app to help people on the Specific Carbohydrate Diet (SCD) check if a food is allowed or not on the diet. This app is endorsed by Kirkton Press Limited, owner of the SCD trademark.

Analysis and machine learning of high-dimensional data from the human gut microbiome.

This repository provides the scripts used to analyze the metagenomics data from the paper Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice.

CMDB Quant Bio Project:Metagenomic pipeline using Kraken2 and Bracken to analyze gut microbiota differences across young, elderly, and centenarian cohorts.

MLGutDB: 阿尔茨海默病(AD)相关肠道微生物整合数据库与分析平台 — 集成 Neo4j 知识图谱 + GraphRAG 智能问答、富集分析、网络分析、疾病分类、聚类与预测分析，支持文献证据追溯与 NCBI/BacDive 官方数据库联动

A computational pipeline for microbiome analysis that identifies differential microbial abundance and visualizes community structure. Demonstrates bioinformatics workflows using Python, pandas, and statistical visualization on simulated ecological data

Automation of Shotgun Metagenome Analysis from Public Data Repositories

Vectorization and Unsupervised Learning of Mouse Operation Taxonomic Units to determine which species of bacteria form distinct groups in a dataset.

A reproducible nf-core/ampliseq pipeline characterizing antibiotic-mediated gut dysbiosis via paired-end 16S rRNA (V4) sequencing. Implements DADA2 exact sequence variant inference, SILVA-based taxonomic classification, and multivariate ecological ordination to quantify compositional perturbations in human fecal microbiomes.