/Faecalibacterium_paper

Primary LanguageR

Differential analysis code

This repository contains the differential analysis R code used in the paper titled: "Human commensal Faecalibacterium prausnitzii ameliorates chronic kidney disease in mice through the gut microbiota-butyrate-renal GPR43 axis"

Installing the required packages

To install the required packages, use the following code:

install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install("edgeR")

To reproduce the results

  • Replace CodeDirectory in the code line 23 with the directory of the Diff_analysis.R file on your machine
  • Prepare two csv files for each dataset named as "[ds_name]_data.csv" & "[ds_name]_meta.csv" for count and metadata respectively. For example, for the dataset "CKD-AmericanHuman," the required files are CKD-AmericanHuman_data.csv & CKD-AmericanHuman_meta.csv
  • Place the data files in the same directory of the Diff_analysis.R file.

Output results:

A folder for each dataset (with the same dataset name) will be created, and the corresponding output will be generated inside these folders. For example, for the dataset "CKD-AmericanHuman," a folder with the name "CKD-AmericanHuman" will be created. The output files will be as follows:

  • normalized counts.csv: for normalized counts using DSeq2 normalization factors.
  • for each contrast, a file will be generated named [contrast]_de_ALL.csv that contains the differential analysis data. For instance, for a contrast between "CKD" & "Control," the file will be named "CKD_vs_Control_de.ALL.csv"