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

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.

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.

A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings are specific for our compute resources

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

Analysis for amplicon data

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

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This repository is a place for codes I have used during my PhD for microbiome analysis of spider egg sacs. Two species were analysed: Parasteatoda tepidariorum and Pardosa lugubris. Three egg sac's conditions: environment + silk + eggs. This code was created in this 'simple adaptation' vibes, so I can tweak it here and there for the future studies.

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

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

Script repository related to the data processing and analyses of the study: "Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes".

This was created and refined during my PhD as the part of the scientific project. Codes are highly customizable. Watch out - Each code does a heatmap for absolutely different thing.