A set of R scripts for the analysis of microbial profiles
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Updated
Feb 7, 2018 - R
A set of R scripts for the analysis of microbial profiles
Data and analysis code for the Indian gut microbiota study
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
Association Between Gut Microbiota and Hypertension
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.
Package Containing Utility-functions to Work with Microbiota-data.
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output
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
The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
biomeUtils is Module-01 of the RIVM-ToolBox. R pkg with common utilities for microbiome research done at the RIVM.
ECCMID 2024 Abstract #04375. Code used to perform the analysis and figures.
Accurate sample inference from amplicon data with single nucleotide resolution
Make Picrust2 Output Analysis and Visualization Easier
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
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.
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