This is the repository for R scripts used in the analysis of 16S rRNA microbiome data analysis generated in the FMT trial from the EU Innovation Action project AVANT.
updated 11/06/2023, Mattia Pirolo
To examine the impact of transplanting feces or gastric content on health and growth parameters and paraclinical parameters in recipient single-housed piglets exposed to a weaning transition and challenged with enterotoxigenic Escherichia coli (ETEC).
This folder contains all datafiles:
- ps_FMT.rds: phyloseq object in R data format for the analysis
- metadata.tsv: tab-separated values file with relevant metadata for the analysis
This folder contains all R scripts:
- composition.R: R script for visualization of taxonomic composition
- diversity.R: R script for alpha- and beta-diversity analysis
- DESeq2.R: R script for differential abundance analysis using DESeq2