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
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 scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings are specific for our compute resources
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
Script repository related to the data processing and analyses of the study: "Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes".
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.
Scripts to convert correlation and p-value matrices to edge list and network
Data analysis of a unique microbiome data set
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