0. Initializing_WorkEnvironment.Rmd

---
title: "0. Initializing_workenvironment"
author: "Baptiste Oosterlinck"
date: "12/13/2021"
output: html_document
---

Setting seed for reproducibility across runs of the script

```{r setup, include=FALSE}
set.seed(1995)
```

Loading the required packages

```{r setup, include=FALSE}
devtools::install_github('https://github.com/paulvanderlaken/ppsr')

packages = c("dada2", "phyloseq", "Biostrings","gridExtra","ggplot2","DECIPHER","phangorn","readxl","tidyverse","ggpubr","vegan","microbiome","tidyr","ggplot2","ggpubr","ALDEx2","dplyr","biomformat","viridis","survminer","survival","data.table","cooccur","visNetwork","tidygraph","ggraph","magrittr","ppsr","boot")

# Packages loading
invisible(lapply(packages, library, character.only = TRUE))
rc <- dada2:::rc

rm(packages)
```

Setting the working directories for the analysis
  - the reference database can be found at: http://www2.decipher.codes/Downloads.html
  - the metadata file was uploaded as supplementary file of the article (DOI: )

```{r setup, include=FALSE}
wd_dir <- #"set working directory"
refDB_path <- "./RefDB/SILVA_SSU_r138_2019.RData" #set path to DECIPHER formated reference database
fastq_dir <- "./Fastq" #set path to the directory with the fastq files

#Clinical data file
meta_file <- "./MetaData.xlsx" #set path to metadata file
```