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      RNA-Seq Analysis

Home
Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
RNA Sequencing Technologies - Dr. Lutz Froenicke
Support
Zoom
Slack
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI
R
Cluster Computing
Data Reduction
Files and Filetypes
Prepare dataset
Preprocessing raw data
Indexing a Genome
Alignment with Star
Generating counts tables
Alignment/Counts with Salmon (Extra)
Data analysis
Prepare R for data analysis
Annotation from BioMart
Differential Expression Analysis
DE Quizzes R Code
Pathway Analysis
Enrichment Quizzes R Code
Comparison between STAR and Salmon
ETC
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

Create a new RStudio project

Open RStudio and create a new project, for more info see Using-Projects

Learn more about renv

Install the needed R packages

Set some options and make sure the packages edgeR, gplots, RColorBrewer, topGO, KEGGREST, Rgraphviz and org.Mm.eg.db are installed (if not install it), and then load

In the R console run the following commands

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

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

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

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

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

if (!any(rownames(installed.packages()) == "org.Mm.eg.db")){
  BiocManager::install("org.Mm.eg.db")
}
library(org.Mm.eg.db)

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

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

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-June-RNA-Seq-Analysis/master/data_analysis/DE_Analysis_mm.Rmd", "DE_Analysis_mm.Rmd")

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

This is the the counts file generated after running Generating counts tables.

I’ve also uploaded to the github repo. In the R console run the following command.

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2021-June-RNA-Seq-Analysis/master/datasets/rnaseq_workshop_counts.txt", "rnaseq_workshop_counts.txt")
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2021-June-RNA-Seq-Analysis/master/datasets/ensembl_mm_104.tsv", "ensembl_mm_104.tsv")

For the salmon datasets

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2021-June-RNA-Seq-Analysis/master/datasets/rnaseq_salmon_workshop_counts.txt", "rnaseq_salmon_workshop_counts.txt")

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: "RNAseq Data Analysis in R"
author: your_name
date: current_date
output:
    html_notebook: default
    html_document: default
---