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/bacillus_minerals.git

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

1.1.2 Libraries

Install this packages if needed

## Bioconductor packages
#https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

requiredPackages = c('edgeR','DESeq2','vsn', "knitr", "rtracklayer", 'clusterProfiler')
for (p in requiredPackages) {
  if(p %in% rownames(installed.packages()) == FALSE) {BiocManager::install(p)}
}

## CRAN packages
requiredPackages = c('ggplot2','dplyr','NMF','grDevices', "hexbin", "statmod", "reshape2")
for (p in requiredPackages) {
  if(p %in% rownames(installed.packages()) == FALSE) {install.packages(p)}
}

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(ggtext)
library(tibble)
library(stringr)
library(dplyr)
library(edgeR)
library(ggplot2)
library(vsn)
library(NMF)
library(grDevices)
library(hexbin)
library(statmod)
library(reshape2)
library(pheatmap)
library(tibble)
library(vegan)
library(limma)
library(GenomicRanges)
library(rtracklayer)
library(clusterProfiler)
library(GenomicRanges)
library(UpSetR)

  1. University of Copenhagen, ↩︎