A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

Microbiome data are challenging to analyse. Development of tools and resources for microbiome data science are ever increasing. This website is a resource for researchers to know about the available tools and resources. This is in no way a complete list and we try our best to search, identify and list the tools and resources.

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Adaptive gPCA A method for structured dimensionality reduction
Ampvis2 Tools for visualising amplicon sequencing data
AMR An R Package for Working with Antimicrobial Resistance Data
ANCOM/ANCOM-BC R package for Analysis of Composition of Microbiomes (ANCOM-BC)
animalcules R shiny app for interactive microbiome analysis
ALDEx2 Analysis Of Differential Abundance Taking Sample Variation Into Account
adaANCOM Transformation and differential abundance analysis of microbiome data incorporating phylogeny


BDMMA Batch Effects Correction for Microbiome Data With Dirichlet-multinomial Regression
BEEM BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data
biome-shiny GUI for microbiome visualization, based on the shiny package “microbiome”
bootLong The Block Bootstrap Method for Longitudinal Microbiome Data
breakaway Species Richness Estimation and Modeling
benchdamic benchmarking of differential abundance methods for microbiome data
BiomeHorizon Visualizing Microbiome Time Series Data in R


CCREPE Compositionality Corrected by PErmutation and REnormalization
corncob Modeling microbial abundances and dysbiosis with beta-binomial regression
curatedMetagenomicData Accessible, curated metagenomic data through ExperimentHub
CoDaSeq Functions for compositional analysis of high throughput sequencing
C3NA correlation and consensus-based cross-taxonomy network analysis for compositional microbial data
CoDaCoRe Learning Sparse Log-Ratios for High-Throughput Sequencing Data
cmmb A Compositional Mediation Model for Binary Outcome: Application to Microbiome Studies


dacomp Testing for Differential Abundance in Compositional Counts Data, with Application to Microbiome Studies
DADA2 Divisive Amplicon Denoising Algorithm
DECIPHER Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R
DECIPHER/IIDTAXA IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
decontam Simple Statistical Identification and Removal of Contaminant Sequences in Marker-Gene and Metagenomics Data
DESeq2 Differential expression analysis for sequence count data
diffTop Differential topic analysis
DivNet An R package to estimate diversity when taxa in the community cooccur via a ecological network
DMBC A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis With Microbial Compositions
dysbiosisR Calculate Microbiome Dysbiosis


edgeR empirical analysis of DGE in R
endoR Interpreting tree ensemble machine learning models with endoR
EasyMicroPlot An Efficient and Convenient R Package in Microbiome Downstream Analysis and Visualization for Clinical Study
EzMAP Easy Microbiome Analysis Platform


FuncDiv Contributional diversity of joint taxa-function data


GLMMMiRKAT A distance-based kernel association test based on the generalized linear mixed model
GMEmbeddings An R Package to Apply Embedding Techniques to Microbiome Data
ggpicrust2 integrates pathway annotations and 10 DA methods


igraph Network Analysis and Visualization in R
iNMF A zero-inflated non-negative matrix factorization for the deconvolution of mixed signals of biological data


labdsv Ordination and Multivariate Analysis for Ecology
LinDA [A log-normal regression and differential abundance too for counts data that corrects for library size to infer the nature of zeros] (https://github.com/zhouhj1994/LinDA) LOCOM A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control
LDM A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome


MaAsLin2 MaAsLin2: Microbiome Multivariate Association with Linear Models
mare Microbiota Analysis in R Easily
massMap A Two-Stage Microbial Association Mapping Framework With Advanced FDR Control
mbtools Collection of R tools to analyze microbiome data
MDiNE MDiNE: a model to estimate differential co-occurrence networks in microbiome studies
MDPbiome MDPbiome: microbiome engineering through prescriptive perturbations
mEQO Ensemble Quotient Optimization for microbiome
MedTest A Distance-Based Approach for Testing the Mediation Effect of the Human Microbiome
MegaR An Interactive R Package for Metagenomic Sample Classification and Disease Prediction using Microbiota and Machine Learning MelonnPan Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
metabaRpipe A DADA2 python container to quickly process 16S amplicons Metacoder An R package for visualization and manipulation of community taxonomic diversity data
metagenomeSeq Differential abundance analysis for microbial marker-gene surveys
MetaLonDA METAgenomic LONgitudinal Differential Abundance method
metamicrobiomeR Analysis of Microbiome Relative Abundance Data using Zero Inflated Beta GAMLSS and Meta-Analysis Across Studies using Random Effects Model
metaSPARSim An R tool for 16S rRNA-gene sequencing count data simulation
MiATDS A powerful adaptive microbiome-based association test for microbial association signals with diverse sparsity levels microbiome R package Tools for microbiome analysis in R MicrobiomeDDA An Omnibus Test for Differential Distribution Analysis of Microbiome Sequencing Data MicrobiomeExplor An R package for the analysis and visualization of microbial communities
MicrobiomeHD A standardized database of human gut microbiome studies in health and disease Case-Control microbiomeMarker R package for microbiome biomarker discovery
MicrobiomeProfiler An R/shiny package for microbiome functional enrichment analysis
MicrobiomeR MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows
MicrobiomeStat MicrobiomeStat: Statistical Methods for Microbiome Compositional Data
microbiomeutilities Extending and supporting package based on microbiome and phyloseq R package
microbiotaPair An R Package for Simplified Microbiome Analysis Workflows on Intervention Study
MicrobiotaProcess MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome
MicroBVS Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package
microDecon An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing
MicroNiche An R package for assessing microbial niche breadth and overlap from amplicon sequencing data
microRMS Reduced metagenome sequencing for strain-resolution taxonomic profiles
microshades An R Package for Improving Color Accessibility and Organization of Microbiome Data
microViz An R package for for analysis and visualization of microbiome sequencing data MiDAT An adaptive direction-assisted test for microbiome compositional data
miLineage A General Framework for Association Analysis of Microbial Communities on a Taxonomic Tree MIMOSA2 A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data mina Microbial community dIversity and Network Analysis with mina
MINT Multivariate INTegrative method
MiRKAT-MC A Distance-Based Microbiome Kernel Association Test With Multi-Categorical Outcomes
mixDIABLO Data Integration Analysis for Biomarker discovery using Latent variable approaches for ’Omics studies
mixMC Multivariate Statistical Framework to Gain Insight into Microbial Communities
MMinte Methodology for the large-scale assessment of microbial metabolic interactions (MMinte) from 16S rDNA data
MTA Microbial trend analysis (MTA) for common dynamic trend, group comparison and classification in longitudinal microbiome study
MZINBVA Variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys


NMIT Microbial Interdependence Association Test–a Non-parametric Microbial Interdependence Test
NetCoMi Network construction and comparison for microbiome data in R
NBZIMM Negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis


OMiSA Optimal Microbiome-based Survival Analysis (OMiSA)
OmicsLonDA Robust identification of temporal biomarkers in longitudinal omics studies


pathostat Statistical Microbiome Analysis on metagenomics results from sequencing data samples - support deprecated phylofactor Phylogenetic factorization of compositional data
phylogeo Geographic analysis and visualization of microbiome data
phyloMDA an R package for phylogeny-aware microbiome data analysis
phyloseq Import, share, and analyze microbiome census data using R
Pldist Pldist: Ecological Dissimilarities for Paired and Longitudinal Microbiome Association Analysis
powmic Power assessment in microbiome case-control studies
POST Phylogeny-guided microbiome OTU-specific association test (POST) PQLSeq An efficient tool designed for differential analysis of large-scale RNA sequencing (RNAseq) data and Bisulfite sequencing (BSseq) data in the presence of individual relatedness and population structure prokounter Differential richness inference for 16S rRNA marker gene surveys


qgraph Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
qiime2R Importing QIIME2 artifacts and associated data into R sessions
qiimer R tools compliment qiime


RAM R for Amplicon-Sequencing-Based Microbial-Ecology
Rbec a tool for analysis of amplicon sequencing data from synthetic microbial communities
RCM A unified framework for unconstrained and constrained ordination of microbiome read count data
RevEcoR Reverse Ecology analysis in R
Rhea A pipeline with modular R scripts
RobZS Sparse least trimmed squares regression with compositional covariates for high dimensional data


selbal Balances: a New Perspective for Microbiome Analysis
ShinyPhyloseq Web-tool with user interface for Phyloseq
SIAMCAT Statistical Inference of Associations between Microbial Communities And host phenoTypes
SigTree Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree
SparseMCMM Estimating and testing the microbial causal mediation effect with the high-dimensional and compositional microbiome data (SparseMCMM)
SPIEC-EASI Sparse and Compositionally Robust Inference of Microbial Ecological Networks
SplinectomeR SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies
StructFDR False Discovery Rate Control Incorporating Phylogenetic Tree Increases Detection Power in Microbiome-Wide Multiple Testing
structSSI Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data
specificity an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data


Tax4Fun Predicting functional profiles from metagenomic 16S rRNA gene data
Tax4Fun2 Prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences
taxize Taxonomic Information from Around the Web
TreeSummarizedExperiment An extension class of SummarizedExperiment to allow hierarchical structure on the row or column dimension
themetagenomics Exploring Thematic Structure and Predicted Functionality of 16S rRNA Amplicon Data
tidyMicro A pipeline for microbiome data analysis and visualization using the tidyverse in R
Tweedieverse Differential analysis of omics data based on the Tweedie distribution
timeOmics An R package for longitudinal multi-omics data integration


vegan R package for community ecologists


yingtools2 Tools and functions for working with clinical and microbiome data


zeroSum Reference Point Insensitive Molecular Data Analysis
ZIBBSeqDiscovery A Zero-inflated Beta-binomial Model for Microbiome Data Analysis

Microbiome data sets

  1. HMP16SData Efficient Access to the Human Microbiome Project through Bioconductor
  2. HMP2Data 16s rRNA sequencing data from the Human Microbiome Project 2
  3. microbiomeDataSets Experiment Hub based microbiome datasets
  4. curatedMetagenomicData Accessible, curated metagenomic data through ExperimentHub

Help us spread information about tools for microbiome data analytics by sharing it with others too!
You can cite this resource as:
Shetty, Sudarshan A., and Leo Lahti. Microbiome data science. Journal of biosciences 44, no. 5 (2019): 115.

Do you want to join us and contribute to the open source microbiome community?

We are working on an open source project developing R/Bioc methods, benchmarking data, and educational material for microbiome research based on the SummarizedExperiment class and its derivatives.
More information please check our website R/Bioc microbiome ecosystem with SummarizedExperiment


  • The Academy of Finland (Grants 295741; 307127)
  • The SIAM Gravitation Grant 024.002.002
  • UNLOCK project of the Netherlands Organization for Scientific Research (NWO)
  • University of Turku, Department of Mathematics and Statistics
  • Molecular Ecology group, Laboratory of Microbiology, Wageningen University, The Netherlands
  • Medische Microbiologie en Infectiepreventie, University Medical Center Groningen, The Netherlands



Site format from Dr. Emily C. Zabor