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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A
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
B
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
C
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
D
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
E
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
F
FuncDiv Contributional diversity of joint taxa-function data
G
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
I
igraph Network Analysis and
Visualization in R
iNMF A zero-inflated
non-negative matrix factorization for the deconvolution of mixed signals
of biological data
L
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
M
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
N
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
O
OMiSA Optimal
Microbiome-based Survival Analysis (OMiSA)
OmicsLonDA Robust
identification of temporal biomarkers in longitudinal omics
studies
P
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
Q
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
R
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
S
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
T
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
V
vegan R package for community ecologists
Y
yingtools2 Tools and functions for working with clinical and microbiome data
Z
zeroSum Reference
Point Insensitive Molecular Data Analysis
ZIBBSeqDiscovery A
Zero-inflated Beta-binomial Model for Microbiome Data Analysis
Microbiome data sets
- HMP16SData Efficient
Access to the Human Microbiome Project through Bioconductor
- HMP2Data 16s
rRNA sequencing data from the Human Microbiome Project 2
- microbiomeDataSets Experiment
Hub based microbiome datasets
- curatedMetagenomicData Accessible, curated metagenomic data through ExperimentHub
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You can cite this resource as:
Shetty, Sudarshan A., and Leo Lahti. Microbiome
data science. Journal of biosciences 44, no. 5 (2019): 115.
Pre-print
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
Acknowledgments
- 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
