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
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Updated
Jun 10, 2024 - R
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
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
An ensemble of functions for easier and quicker preliminary microbiome analyses
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
Make Picrust2 Output Analysis and Visualization Easier
Accurate sample inference from amplicon data with single nucleotide resolution
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
A set of R scripts for the analysis of microbial profiles
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