Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

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

Comparative Metatranscriptomics Workflow

Mothur procedures for 16S and ITS analysis

The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.

A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.

Analysis for amplicon data

Use one command to perform genome-centric metagenomics using state-of-the-art methods

This repository contains all codes used in the "The Gastric Microbiome and Gastric Carcinogenesis: Bacterial Diversity, Co-occurrence Patterns and Predictive Models" projects

Analysis of the gut microbiome of Amyotrophic Lateral Sclerosis (ALS) patients using the DADA2 workflow

Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2

A repository containing a demo microbiome workflow for R and Python

A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG

short-read amplicon data visualization suite

Microbiome analysis pipeline with reference tutorial. This code was written in October 2024 to process rRNA marker gene data (16S and ITS) from rhizosphere soil samples.

Script repository related to the data processing and analyses of the study "Evidence of habitat specificity in sponge microbiomes from Antarctica"

Data analysis of a unique microbiome data set

Scripts to convert correlation and p-value matrices to edge list and network