Chapter 1 Introduction

This ‘book’ is written to explain the use of the DE4Rumi package, developed to automate many of the steps for simple Differential Expression (DE) analysis, but also includes further analyses that were used in my thesis.
The DE4Rumi package is basically a set of wrappers for other well-known packages, particularly the DESeq2 package (Love, Anders, and Huber 2021). This package allows substantial customisation, but also uses sensible defaults for beginners. This is also helpful for users who wish to quickly inspect the quality of their RNAseq data with a ‘rough’ analysis before customising their functions further.

This book is targeted at beginner R users, but for specific help on functions please see the help files for each function. This can be accessed by typing ?function_name for the name of the function into the R Console.

1.1 Installing DE4Rumi Package

The package is hosted on github and not on an official repository. Therefore, it is considered a ‘development’ package. To install it you will first need to install the devtools package:

install.packages("devtools")

Then, use the install_github() function to install it by using the following code:

devtools::install_github("davos-i/DE4Rumi")

To view the package on GitHub go to: https://github.com/davos-i/DE4Rumi

References

Love, Michael, Simon Anders, and Wolfgang Huber. 2021. DESeq2: Differential Gene Expression Analysis Based on the Negative Binomial Distribution. https://github.com/mikelove/DESeq2.