microbiota

Make Picrust2 Output Analysis and Visualization Easier

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.

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

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

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

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

Comprehensive KEGG Data Retrieval Using Multiple Sources

📓 Minimal cheatsheet for functions in the phyloseq R package

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

Data and analysis code for the Indian gut microbiota study

Meta-analysis on human gut microbiota in Colorectal cancer

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.

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

The Celiac Microbiome Repository is a comprehensive collection of all available gut microbiome sequencing datasets that include individuals with celiac disease.

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"