A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
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Updated
Apr 11, 2023 - CSS
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Python package to study microbial communities using metabolic modeling.
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
Make Picrust2 Output Analysis and Visualization Easier
Open-source opinionated Galaxy-based framework for microbiota analysis
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
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"
Notebooks and files necessary to replicate the graphs and analyses presented in the Preprint, doi: 10.1101/2020.09.29.20203638
This repository provides scripts for the 16S microbiome analysis and metagenome prediction using linux and R-Studio
A set of R scripts for the analysis of microbial profiles
R scripts used for analysis of data reported in Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls
biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.
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