Change log

List of R tools for microbiome data analysis

Change log 11 April, 2023

• Microbiome Tools
  • ggpicrust2
    
  • mEQO

Change log 28 December, 2022

• Microbiome Tools
  • adaANCOM
    
  • benchdamic
    
  • C3NA
    
  • microshades
    
  • GMEmbeddings
    
  • prokounter
    
  • LOCOM
    
  • endoR
    
  • specificity
  • OmicsLonDA
  • LDM
    
  • POST
    
  • phyloMDA
    
  • MiDAT
    
  • BiomeHorizon
    
  • dysbiosisR
    
  • MiRKAT-MC
    
  • EasyMicroPlot
    
  • MIMOSA2
    
  • MZINBVA
    
  • timeOmics
    
  • CoDaCoRe
    
  • cmmb
    
  • MiATDS
    
  • RobZS
    
  • Tax4Fun2
    
  • EzMAP
    
  • iNMF
    
  • microRMS
• Other Tools
  • DataExplorer

Change log 24 December, 2021

• Tutorials and Educational Resources
  • Hannah Freund. Amplicon Analysis Workflow
    
  • Tully, B. J. et al. BVCN
    
• Microbiome Tools
  • MicrobiomeStat
    
  • Rbec
    
  • AMR
    
  • MicrobiomeProfiler
    
  • Tweedieverse
    
  • MINA
    
• Other Tools
  • TreeHeatmap
    
  • Fastverse

Change log 13 October, 2021

• Other Tools
  • Added gggenes, gggenomes
    
  • Added ggplot2 gallery
    
• Microbiome Tools
  • rANOMALY
    
  • SuRF
    
  • timeOmics
    
  • CMMB
    
  • MiATDS
    
  • RobZS

Change log 11 September, 2021

• Added Contributors section
  
• Added resources new 8 to 10
  
• Added ‘Additional’ resources suggested by Svetlana UP to Controls section
  
• Added OTU/ASV debate Controls section

Change log 08 August, 2021

• Tools
  • diffTop and microeco added
    
• GitHub actions testing for website rendering

Change log 04 August, 2021

• Added Tutorials and Educational Resources

Change log 22 May, 2021

• Revamped website
  
• Tools
  • metaSPARSim added
    
• References for Controls in Microbiome Research

Change log 07 May, 2021

• Tools
  • ANCOM-BC added next to ANCOM
    
  • ALDEx2 Analysis Of Differential Abundance Taking Sample Variation Into Account
    
  • CoDaSeq Functions for compositional analysis of high throughput sequencing
    
  • DivNet An R package to estimate diversity when taxa in the community cooccur via a ecological network

Change log 20 March, 2021

• Tools
  • 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
    
  • 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
    
  • selbal Balances: a New Perspective for Microbiome Analysis
    
  • tidyMicro A pipeline for microbiome data analysis and visualization using the tidyverse in R
• 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
• Other tools
  • Antoni Susin, Yiwen Wang, Kim-Anh Lê Cao, M.Luz Calle.: Variable selection in microbiome compositional data analysis: tutorial
• Reformatted the code for website
  
• Added Changes log
  
• Added Acknowledgments

Shetty, Sudarshan A., and Leo Lahti. Microbiome data science. Journal of biosciences 44, no. 5 (2019): 115.
Pre-print
Zendo: