microbiome R package

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

🦠 A comprehensive R package for deep mining microbiome

Qiita - A multi-omics databasing effort

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

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

The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.

Various functions for analysis of microbial community data

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

The is mostly a wrapper tool using phyloseq and microbiome R packages.

topological data analysis of population-scale microbiomes

Analyses in R and Python Using curatedMetagenomicData

A comprehensive and customizable R package for microbiome analysis.

A Collection of Bioinformatics Projects

Metagenomics calibration R package

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations

iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline