Appendix B — Tools for microbiome analysis

A

Adaptive gPCA A method for structured dimensionality reduction Ampvis2 Tools for visualising amplicon sequencing 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

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

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

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

E

edgeR empirical analysis of DGE in R

F

G

GLMMMiRKAT A distance-based kernel association test based on the generalized linear mixed model

H

HuMMANet Harmonized cross-study resource of human gut microbiome-metabolome associations

I

igraph Network Analysis and Visualization in R

J

K

L

labdsv Ordination and Multivariate Analysis for Ecology

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 microDecon An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing microbiotaPair An R Package for Simplified Microbiome Analysis Workflows on Intervention Study 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 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 microbiome R package Tools for microbiome analysis in R MicrobiomeDDA An Omnibus Test for Differential Distribution Analysis of Microbiome Sequencing Data MicrobiomeHD A standardized database of human gut microbiome studies in health and disease Case-Control microbiomeMarker R package for microbiome biomarker discovery MicrobiomeR MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows microbiomeutilities Extending and supporting package based on microbiome and phyloseq R package MicrobiotaProcess MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome miLineage A General Framework for Association Analysis of Microbial Communities on a Taxonomic Tree MINT Multivariate INTegrative method 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 MicrobiomeExplor An R package for the analysis and visualization of microbial communities MicroBVS Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package MicroNiche An R package for assessing microbial niche breadth and overlap from amplicon sequencing data microViz An R package for for analysis and visualization of microbiome sequencing data

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)

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 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

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 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

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

T

Tax4Fun Predicting functional profiles from metagenomic 16S rRNA gene data 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

U

V

vegan R package for community ecologists

X

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