Chapter 1 Introduction

This webbook contains all the code used for data analysis in study of gut microbiomes of newts across ponds included in a restoration plan.

1.1 Prepare the R environment

1.1.1 Environment

To reproduce all the analyses locally, clone this repository in your computer using:

RStudio > New Project > Version Control > Git

And indicating the following git repository:

https://github.com/alberdilab/pig_stress_hologenomics.git

Once the R project has been created, follow the instructions and code chunks shown in this webbook.

1.1.2 Libraries

The following R packages are required for the data analysis.

# Base
library(R.utils)
library(knitr)
library(tidyverse)
library(devtools)
library(tinytable)
library(rairtable)
library(janitor)
library(broom)
library(purrr)
library(dplyr)
library(tibble)
library(ggplot2)
library(BiocManager)
library(SummarizedExperiment)
library(factoextra)
library(edgeR)
library(limma)
library(DESeq2)
library(VennDiagram)
library(grid)