Microbiome analysis

Accurate sample inference from amplicon data with single nucleotide resolution

Amplicon sequencing analysis workflow using DADA2 and QIIME2

PANDORA 💻

Orchestrating Microbiome Analysis

Make Picrust2 Output Analysis and Visualization Easier

List of software packages for repeated measures analysis in -omics data

Testing differences in cell type proportions from single-cell data.

BioFlowML is a machine-learning toolbox implementing workflows for generating classification models and identification of biomarkers using microbiome data or clinical metadata.

Quantitative metagenomic alignment and taxonomic exact-matching

National Microbiome Data Collaborative (NMDC) unified data model

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

Versatile open-source tool for microbiome analysis

MaAsLin2: Microbiome Multivariate Association with Linear Models

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

Modelling and Inference of MICrobiomes Project (MIMIC) is a Python package dedicated to simulate, model, and predict microbial communities interactions

q2-boots: bootstrapped and rarefaction-based alpha and beta diversity analyses 🥾

Repository containing lists of all published ancient metagenomic (and related) samples and libraries

A comprehensive R toolkit for comparing and evaluating Differential Abundance Analysis (DAA) methods in microbiome studies.