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.

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

Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.

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

OptTaxPro: Optimized Taxonomic Profiling of microbiome using full-length 16S rRNA sequences

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

This is the repository for a bioinformatics project about identifying the optimal pipeline for identifying a potential microbiome shift in COPD patients after ceasing azithromycin treatment.

This script I have created for my last PhD-related paper, as I needed to better understand the microbiome of cocoon's environment, cocoon's silk and cocoon's eggs. It also introduces more refined metagenomic data filtering.

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.

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.

Host plant rhizosphere microbiome analysis

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

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.

General purpose package containing useful functions for microbiome analysis pipelines

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

Workflow of community composition and diversity analyses of bacteria and archaea with QIIME 2