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

Make Picrust2 Output Analysis and Visualization Easier

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

Python package to study microbial communities using metabolic modeling.

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

Open-source opinionated Galaxy-based framework for microbiota analysis

The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

📓 Minimal cheatsheet for functions in the phyloseq R package

Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output

Improved bee microbiota characterization using routine 16S rRNA gene sequencing 🐝🧬

Meta-analysis on human gut microbiota in Colorectal cancer

Data and analysis code for the Indian gut microbiota study

biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.

Microbiome Study of Lupus Patients

Code for reproducing results in the paper: "Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon"

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.