Accurate sample inference from amplicon data with single nucleotide resolution

Make Picrust2 Output Analysis and Visualization Easier

Papers in which I have been involved as data scientist. For the title, info and and/or the DOI of each one of them, check the corrispective "Paper_title_and_info" txt file

An ensemble of functions for easier and quicker preliminary microbiome analyses

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

Scripts and data for the METAolive project

Analyses Pros-RODAM microbiota data

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

ECCMID 2024 Abstract #04375. Code used to perform the analysis and figures.

biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.

The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures

biomeViz is Module-03 of the RIVM-ToolBox. R pkg with data visualization tools for microbiome research done at the RIVM. . Development Phase: Active Development

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

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

Package Containing Utility-functions to Work with Microbiota-data.

A summary of the scripts used in performing quality filtering and data analysis of Illumina high throughout bacterial sequences involved in this freshwater aquatic invertebrate microbiota study.

Association Between Gut Microbiota and Hypertension

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

Data and analysis code for the Indian gut microbiota study