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Metagem ⭐ 155

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

Qiita - A multi-omics databasing effort

Python package to study microbial communities using metabolic modeling.

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

Deepmicrobes ⭐ 61

DeepMicrobes: taxonomic classification for metagenomics with deep learning

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

Woltka: a versatile meta'omic data classifier

Emperor a tool for the analysis and visualization of large microbial ecology datasets

Sample search by metadata and features

Microbiomehd ⭐ 40

Cross-disease comparison of case-control gut microbiome studies

An all-in-one genome-centric metagenomics workflow using long reads

Q2 Qemistree ⭐ 24

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Stag Mwc ⭐ 24

StaG Metagenomic Workflow Collaboration

Ghost Tree ⭐ 23

creating hybrid-gene phylogenetic trees for diversity analyses

Nmdc Schema ⭐ 23

This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.

exploratory and interactive microbiome analyses based on heatmaps

The Microbiome Interpretable Temporal Rule Engine

Bayesian Inferential Regression for Differential Microbiome Analysis

Super Focus ⭐ 19

A tool for agile functional analysis of shotgun metagenomic data

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data

Microbiome Mvib ⭐ 16

Microbiome-based disease prediction with multimodal variational information bottlenecks, Grazioli et al., PLOS Computational Biology 2022

Metasub_cap ⭐ 16

A comprehensive pipeline for short read metagenomic data

The Microbial Co-occurrence Network Explorer

Snakemake workflow for comparison of differential abundance ranks

Phylotoast ⭐ 12

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Snakemake Workflow Qiime2 ⭐ 11

Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2

A spatially explicit trait- and individual-based microbial systems modelling framework

Microbiome Toolbox ⭐ 8

Early Life Microbiome Toolbox

Case-control matching for microbiome data

Detect complete HGT event rapidly and accurately from complex metagenomics data

Snakemake pipeline for microbiome diversity effect size benchmarking

Effect size calculations for microbiome data

Microberx ⭐ 5

GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

Metasequencing ⭐ 5

A metagenomics pipeline using the CGAT framework.

Main repository of the Flint project for Spark and Amazon EMR.

Sample Annotator ⭐ 5

NMDC Sample Annotator

Fratjuice ⭐ 5

Uncovering the microbes of fraternity basements

FOCUS: An Agile Profiler for Metagenomic Data

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