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      Microbial Community Analysis (amplicons)

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Introduction and Lectures
Intro to the Workshop and Core
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What is Bioinformatics/Genomics?
Generating Microbial Amplicons
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Software and Links
Scripts
Prerequisites
CLI
Introduction to R
High Performance Computing
Data Reduction
Filetype Description
MCA project setup
Preprocessing Reads
ASV production
Data Analysis
Prepare Analysis
MCA Part 1
MCA Part 2
MCA Part 3
MCA Part 4
MCA Part 5
MCA Part 6
ETC
Closing thoughts
Github page
Biocore website

Prepare R and copy over the Phyloseq object for Data Analysis

Create a new RStudio project

Open RStudio and create a new project, for more info on project see this page

We first need to make sure we have the necessary packages, and then load each package to veryify they installed correctly

To install the packages, In the R console run the following commands

if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")

if (!any(rownames(installed.packages()) == "phyloseq")){
  BiocManager::install("phyloseq")
}
library(phyloseq); packageVersion("phyloseq")

if (!any(rownames(installed.packages()) == "biomformat")){
  BiocManager::install("biomformat")
}
library(biomformat); packageVersion("biomformat")

if (!any(rownames(installed.packages()) == "ggplot2")){
  BiocManager::install("ggplot2")
}
library(ggplot2); packageVersion("ggplot2")

if (!any(rownames(installed.packages()) == "gridExtra")){
  BiocManager::install("gridExtra")
}
library(gridExtra); packageVersion("gridExtra")

if (!any(rownames(installed.packages()) == "vegan")){
  BiocManager::install("vegan")
}
library(vegan); packageVersion("vegan")

if (!any(rownames(installed.packages()) == "edgeR")){
  BiocManager::install("edgeR")
}
library(edgeR); packageVersion("edgeR")

if (!any(rownames(installed.packages()) == "dada2")){
  BiocManager::install("dada2")
}
library(dada2); packageVersion("dada2")

if (!any(rownames(installed.packages()) == "phangorn")){
  BiocManager::install("phangorn")
}
library(phangorn); packageVersion("phangorn")

if (!any(rownames(installed.packages()) == "tidyr")){
  BiocManager::install("tidyr")
}
library(tidyr); packageVersion("tidyr")

if (!any(rownames(installed.packages()) == "kableExtra")){
  BiocManager::install("kableExtra")
}
library(kableExtra); packageVersion("kableExtra")

Download the template Markdown workshop document and open it

In the R console run the following command

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2021-May-Microbial-Community-Analysis/master/data_analysis/mca_part1.Rmd", "mca_part1.Rmd")

Download the data file for the workshop document and preview/open it

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2021-May-Microbial-Community-Analysis/master/data/phyloseq_nochim_silva.RData", "phyloseq_nochim_silva.RData")

Edit the file YAML portion

The top YAML (YAML ain’t markup language) portion of the doc tells RStudio how to parse the document.

---
title: "Microbial Community Analysis in R"
author: your_name
date: current_date
output:
    html_notebook: default
    html_document: default