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
Data and analysis code for the Indian gut microbiota study
Comprehensive KEGG Data Retrieval Using Multiple Sources
biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
A set of R scripts for the analysis of microbial profiles
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
Accurate sample inference from amplicon data with single nucleotide resolution
An ensemble of functions for easier and quicker preliminary microbiome analyses
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
ECCMID 2024 Abstract #04375. Code used to perform the analysis and figures.
Companion scripts for my PhD thesis in Bioinformatics.
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