Top 21 microbiome open source projects

Sample search by metadata and features

The Microbiome Interpretable Temporal Rule Engine

Schloss Lab Tools for Reproducible Microbiome Research 💩

R package for microbiome biomarker discovery

Qiita - A multi-omics databasing effort

exploratory and interactive microbiome analyses based on heatmaps

Compare different differential abundance and expression methods

Visualize microbiome data with black magic ggtree

Various functions for analysis of microbial community data

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

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

Cross-disease comparison of case-control gut microbiome studies

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Collection of commonly used RDP Tools for easy building

A fast and scalable phylogenetic tree viewer for microbiome data analysis

A model-based visualization method for microbiome data

MaAsLin2: Microbiome Multivariate Association with Linear Models