microbiota

Make Picrust2 Output Analysis and Visualization Easier

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

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

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

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

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

Comprehensive KEGG Data Retrieval Using Multiple Sources

Data and analysis code for the Indian gut microbiota study

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

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

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

A set of R scripts for the analysis of microbial profiles

Scripts and data for the METAolive project

An R package with helper functions to automate microbiome analysis, including alpha and beta diversity, differential abundance analysis with DESeq2, machine learning, mediation analysis, and others.

CMDB Quant Bio Project:Metagenomic pipeline using Kraken2 and Bracken to analyze gut microbiota differences across young, elderly, and centenarian cohorts.

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

Accurate sample inference from amplicon data with single nucleotide resolution

An ensemble of functions for easier and quicker preliminary microbiome analyses

16S sequencing analysis pipeline for low biomass samples