Software and Resources

Phyloseq-based tools
- microbiome R package
  Lahti L, Shetty SA, Blake T and Salojarvi J. (Bioconductor) An R package for microbial community analysis.
  Tutorials can be found here.
- microbiomeutilities
  Shetty SA, Lahti L. (GitHub) Extending and supporting R package based on microbiome and phyloseq.
  A utility package for the parent microbiome R package. Tutorial can be found here
- chkMocks
  Shetty SA. (GitHub) chkMocks is a basic R package for comparing experimental mock communities (positive controls) with theoretical (expected) composition
- syncomR
  Analysis of Synthetic Microbial Communities.
  Handling microbial community (MC) data with special emphasis on time series data from synthetic MCs. Bundles R codes openly available in literature into functions for convenient access.
- dysbiosisR
  The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures.
  The dysbiosisR package is a collection of functions to calculate six dysbiosis measures from microbiota profiling data. The package currently supports microbiome data organized as phyloseq objects.
TreeSummarizedExperiment-based tools
- microbiomeDataSets
  Ernst F, Lahti L, Shetty S (2021). microbiomeDataSets: Experiment Hub based microbiome datasets.
  microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor’s ExperimentHub infrastructure.
- mia
  Ernst F, Shetty S, Borman T, Lahti L (2021). mia: Microbiome analysis
  mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure.

More information on our efforts on expanding the the R/Bioc microbiome ecosystem with SummarizedExperiment

Training

• microbiomeutilities-shiny
Shetty SA, Lahti L. (GitHub)
A web based shiny dashboard for prelimanry analysis of microbial census data.
This shiny app is used for teaching basic 16S rRNA gene based microbial community analysis.

• TeachingMIB20306
Shetty SA. (GitHub)
A web based shiny dashboard for proteomics data analysis.
Teaching MIB20306: This dashboard uses data from Bui, Thi Phuong Nam, Jarmo Ritari, Sjef Boeren, Pieter De Waard, Caroline M. Plugge, and Willem M. De Vos. “Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal.” Nature Communications 6 (2015): 10062. The data has been modified/subsetted for teaching purpose.

Open data and resources

• Shetty SA (2023) Automate Microbiome Analysis Using Quarto

• Lahti L, Shetty SA, Ernst F (2021) Orchestrating Microbiome Analysis

• Shetty SA & Lahti L (2018). A list of R environment based tools for 16S rRNA gene data exploration, statistical analysis and visualization Zenodo. http://doi.org/10.5281/zenodo.1256879.

• Shetty SA, Lahti L, Hermes Gerben DA, & Smidt H. (2018, September 27). Microbial bioinformatics introductory course material 2018 (Version 0.01). Zenodo. http://doi.org/10.5281/zenodo.1436630.

• GitHub repositories: https://github.com/microsud?tab=repositories.

Organization Specific Tools

RIVM-Microbiome-Toolbox
Tools for supporting reproducible microbiome data analysis at RIVM more information