microbiome R package

Make Picrust2 Output Analysis and Visualization Easier

This repo contains the R microshades package, which contains a color blind accessible color palette with 30 unique colors and functions for applying these colors to microbiome data.

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

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

Fantaxtic - Nested Bar Plots for Phyloseq Data

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

A comprehensive and customizable R package for microbiome analysis.

A model-based visualization method for microbiome data

Dadaist2 🟨 Highway to R

accessory functions for processing microbial community data

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

Tutorials for R

📓 Minimal cheatsheet for functions in the phyloseq R package

Mothur procedures for 16S and ITS analysis

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

Create phylogenetic trees from Bracken/Kraken2 reports

How to analyze shotgun metagenomic data with phyloseq - a walkthrough

Microbial Community Analysis with Chipster

dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.