Chapter 1 Introduction

This WebBook contains the code written to analyse data from the study of the functional profile of metagenome-assembled genomes and temporal trends of derived microbial communities from intensively reared broiler chickens.

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/chicken_genome_reduced_bacteria.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(rmarkdown)
library(janitor)

# For tree handling
library(ape)
library(phyloseq)
library(phytools)
library(tidytree)

# For plotting
library(ggplot2)
library(ggrepel)
library(ggpubr)
library(ggnewscale)
library(gridExtra)
library(ggtreeExtra)
library(ggtree)
library(ggh4x)
library(sjPlot)
library(colorspace)
library(vioplot)

# For statistics
library(spaa)
library(vegan)
library(Rtsne)
library(microbiome)
library(geiger)
library(hilldiv2)
library(distillR)
library(broom.mixed)
library(Hmsc)
library(MuMIn)
library(corrplot)
library(lme4)
library(nlme)
library(boot)

  1. University of Copenhagen, ↩︎