Microbiome Abundance Analysis

code to reproduce AIH results

Code that was used to generate figures for the Mahmoudi et al., 2013 publication

Analysis of Salmo trutta gametes and embryo microbiome project in Vals/Trun, Switzerland

🌊 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM

MGSAT semi-automated differential abundance analysis of omics datasets

Analysis scripts for Gortzia yakutica paper

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

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

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

A nextflow pipeline for the analysis of 16S amplicon data built around RExMap

nyankomicro is a in-house package that aims to make the plots more beautiful.

Compare different differential abundance and expression methods

Mothur procedures for 16S and ITS analysis

The is mostly a wrapper tool using phyloseq and microbiome R packages.

accessory functions for processing microbial community data

Meta16s - an all-in-one solution for streamlined 16s analyses

Outlines the process of testing for statistical differences in certain taxa by group utilizing the phyloseq, tidyverse, and various statistical packages within R.