Introduction

This is a tutorial for analyzing RNAseq data using the DESeq2 and other packages from Bioconductor. These tutorial will start explaining different ways for transcript quantification and how to generate gene-level count data sets.

This tutorial is based on:

• The RNA-seq workflow described by the authors of the DESeq2 package. You can find the original workflow here.

• The RNA-seq by example book from the Biostar Handbook Collection

Data used for this tutorial comes from the paper:

• Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae) (https://doi.org/10.1371/journal.pone.0255660).

Packages to be used

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

BiocManager::install(c("DESeq2", "vsn"))

install.packages(c('pheatmap', 'ggpubr', 'RColorBrewer',
                   'ggplot2', 'magrittr', 'dplyr', 'tidyr',
                   'purrr', 'readr'))