dada2

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

Dadaist2 🟨 Highway to R

Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project

A metabarcoding pipeline for analysing Illumina amplicon data.

neonMicrobe: Processing NEON soil microbe marker gene sequence data into ASV tables, duplicated from https://github.com/claraqin/neonMicrobe

Nextflow pipeline for end-to-end taxonomic profiling of paired-end 16S rRNA amplicon data (V3–V4), supporting multiple ASV inference methods and classifiers.

Reproducible code and analyses for a follow-up household-matched case-control study of gut microbiome alterations in canine idiopathic epilepsy.

Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics.

This repository provides a cloud-based learning module for microbial analysis of 16S rRNA sequencing data. It covers principles, data preprocessing, taxonomic classification, and diversity analysis using R and AWS SageMaker.